Federally Qualified Health Centers operate in one of the most demanding healthcare environments. They serve high patient volumes while managing limited budgets, strict compliance rules, and complex reporting needs. An effective EHR is not optional for FQHCs but rather essential for daily operations, long-term funding, and quality patient care.
To identify the best EHR systems for FQHCs, we followed a structured evaluation process. Our evaluation included hands-on testing and direct feedback from community health centers. We prioritized platforms that support UDS reporting, compliance tracking, and FQHC-specific billing workflows. We also focused on usability, scalability, and support for limited IT resources. We identified the 9 leading EHR solutions designed specifically for Federally Qualified Health Centers.
Software | Rating | Trial Info | Pricing | Best For | Main Features |
Epic EMR-(Editor's Choice) | 4.4/5 | No free trial available View Demo | $5,000 to $7,000/physician Get a Custom Quote | Remote patient monitoring |
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3.9/5 | No free trial available View Demo | $299/provider/month Get a Custom Quote | Population health insights |
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3.9/5 | No free trial available View Demo | Custom Pricing Get a Custom Quote | FHIR and TEFCA interoperability |
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3.4/5 | No free trial available View Demo | $449/month/provider Get a Custom Quote | Medical AI scribe Sunoh.ai |
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4.1/5 | No free trial available View Demo | $118/month Get A Custom Quote | PHR portal |
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4/5 | No free trial available View Demo | Custom Pricing Get a Custom Quote | Medicare prospective payment |
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3.5/5 | No free trial available View Demo | Custom Pricing Get a Custom Quote | Personalized workflows |
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3.6/5 | No free trial available View Demo | Custom Pricing Get a Custom Quote | UDS, PCMH reporting |
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3.3/5 | No free trial available | $295/provider/month Get a Custom Quote | Automated rate adjustments |
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1. Epic- Editor’s Choice
When it comes to EHR systems used by Federally Qualified Health Centers, Epic stands out as an enterprise-grade platform adopted by large FQHC networks and look-alike organizations. While not built exclusively for FQHCs, Epic supports high patient volumes, integrated care models, and multi-site operations. Moreover, many FQHCs access Epic through Community Connect or OCHIN partnerships, which help manage HRSA and UDS reporting needs. Additionally, Epic connects medical, behavioral, and specialty services within one record.
Pros | Cons |
Centralized storage and accessibility of patient data and medical history Provides robust patient monitoring features for practice management Meaningful use certification, ensuring adherence to industry standards Improves patient engagement through the patient portal feature | Requires initial training to navigate the system effectively Users may experience information overload due to extensive patient data across many integrated modules |
Best For
The software is designed for hospitals, health systems, medical schools, and a wide range of specialties such as dental, genetics, endoscopy, etc.
Key Features
- Revenue Cycle Management
- Schedule Appointments
- Self-Service Portal
- Reporting And Analytics
- Charting
- Practice Management
Pricing
Epic pricing is customized with prices starting at $5,000 to $7,000/physician. Users can get a custom quote based on organizations’ size and requirements.
Disclaimer: The pricing has been sourced from third-party websites and is subject to change.
Why We Like It
Epic’s interoperability capabilities allow hospitals to share patient information seamlessly across departments and external care partners. Its Care Everywhere network exchanges millions of patient records daily, enabling clinicians to access comprehensive histories from other providers, labs, and imaging centers.
User Ratings
Epic is rated 4.4/5 based on extensive user feedback. Users appreciate the ease when it comes to finding important information within patient charts. However, a few users think that the scanning feature of the software could be improved.
2. NextGen
NextGen Healthcare offers an EHR platform well-suited for Federally Qualified Health Centers (FQHCs) and community health centers. The system supports visit-based workflows, comprehensive documentation, and integrated care. NextGen supports UDS+, HRSA, CMS, and value-based reporting in one workflow, helping FQHCs manage high patient volumes with limited administrative resources. Scalable across multiple sites, NextGen provides robust patient engagement, billing, and interoperability functions that align with the operational and regulatory demands typical of FQHC environments.
Pros | Cons |
Easy to navigate and simple to learn, ensuring quick user adoption Responsive and supportive account representatives who address issues promptly Efficient filing features that simplify document separation, even after scanning into the system Enables efficient employee tracking and care management Offers managed cloud hosting, providing reliable performance and scalability | Lack of clarity between the platform and clearinghouse often leads to confusion and delays Limited MIPS/MACRA measurement capabilities, making compliance tracking challenging |
Best For
NextGen is designed for various specialties like urology, ophthalmology, podiatry, pulmonology, rheumatology, etc. to meet clinical and financial goals of healthcare organizations.
Key Features
- AI Features
- Dashboard
- Patient Portal
- Interoperability
- Optimized Appointments
- Clinical Summaries
- Electronic Prescription
- AI-Powered Documentation
Pricing
While NextGen cost is based on the specialty, number of users, and the various modules selected, generally its pricing starts at $299/provider/month.
Disclaimer: The pricing has been sourced from third-party websites and is subject to change.
Why We Like It
Seamless interoperability is a key feature for FQHCs using NextGen. It allows community health centers, hospitals, ambulatory surgery centers, and even non‑NextGen systems to communicate and share patient data effortlessly. This connectivity ensures complete patient treatment, smooth care coordination across multiple sites, and reduces duplicated tests, helping FQHCs close care gaps and improve overall patient outcomes.
User Ratings
NextGen is rated 3.9/5 based on user feedback. Users like the AI assist feature as it helps them in taking notes easily and efficiently. However, some reviews complain that live training sessions are very limited.
3. athenaOne
athenaOne, a comprehensive EHR and practice management platform, is built to support community health centers and FQHCs. It supports value‑based care and complex reporting requirements like HCC/RAF, HEDIS, and UDS/UDS+ while ensuring compliance with ONC HIT standards. An FQHC finance manager reviews monthly revenue performance across multiple sites. Using FQHC activity reporting, the manager tracks PPS payments and encounter codes in one view. The AR aging tools highlight delayed or underpaid claims. This visibility helps the team resolve issues faster, improve cash flow, and ensure accurate reimbursement under FQHC payment rules.
Pros | Cons |
Tailored EHR platform allows customization to specific specialty needs Automated workflows help reduce administrative burdens and improve efficiency Telehealth services facilitate virtual care delivery | Initial training may be required Dependency on reliable internet connectivity for cloud-based features |
Best For
athenaOne is used by provider organizations, healthcare payers, behavioral health specialists, orthopedics, pediatrics, etc.
Key Features
- Electronic Health Record (EHR)
- Patient Engagement
- Revenue Cycle Management
- Medical Billing
- Telehealth
- Reporting And Analytics
Pricing
athenaOne pricing can be customized and varies based on practice size, claim volume, and complexity.
Disclaimer: The pricing is subject to change.
Why We Like It
athenaOne’s CHC financial reporting offers detailed visibility into PPS payments and FQHC encounter codes. Its FQHC activity reporting helps centers track and manage patient visits efficiently. The AR aging tools provide insight into accounts receivable, supporting better revenue management and compliance.
User Ratings
athenaOne is rated 3.9/5 based on several reviews. For users, the well-organized homepage lets them have access to important information whenever they need it. Some reviewers think that reading appointment notes on mobile is a hassle and needs to be improved.
4. eClinicalWorks
eClinicalWorks offers a comprehensive EHR platform tailored to health centers and FQHCs that need strong clinical workflows, reporting, and care coordination. Within the software, users can find Ryan White Reporting to document and finalize all the relevant data. An FQHC quality manager prepares weekly UDS submissions and performance reviews. Instead of pulling data manually from multiple modules, the team relies on automated UDS reporting and analytics within eClinicalWorks.
Pros | Cons |
Automates administrative tasks to help healthcare providers improve patient care Sends automated appointment reminders to reduce no-shows Highly customizable for provider needs | Some users may find the software difficult to learn and use May not be compatible with some healthcare software systems or devices |
Best For
The software is designed for various specialties such as ob/gyn, dental, behavioral health, and urgent care.
Key Features
- Population Health Management
- Appointment Scheduling
- Patient Portal
- E-Prescribing Features
- Clinical Decision Support
Pricing
eClinicalWorks pricing starts at $449/month per provider with the following options.
- EHR Only – $449/month/provider
- EHR with Practice Management – $599/month/provider
- RCM as a Service – 2.9% of practice collections
Disclaimer: The pricing is subject to change.
Why We Like It
eClinicalWorks enables health centers to capture patient demographic data easily. This feature helps establish eligibility under federal poverty guidelines. It also allows clinics to set up sliding fee schedules, supporting access to care and financial management for underserved populations.
User Ratings
The software is rated 3.4/5 based on a number of reviews. Users appreciate the data portability this software has to offer, offering them ease. Though some users think that the software's visuals could be upgraded.
5. RXNT
RXNT helps FQHCs reduce administrative workload, stay compliant, and focus more on patient care. Its integrated EHR, billing, and e-prescribing tools support Medicaid and Medicare rules, sliding fee schedules, and FQHC-specific reimbursement models. With configurable workflows, real-time patient discounts, accurate coding, and predictable pricing that includes implementation and unlimited support, RXNT offers a practical, cost-effective solution for community health centers.
Pros | Cons |
Offers automated billing tools that help practices improve revenue and reduce manual work Delivers flexible customization to support different specialties and care environments Streamlines medication management with efficient, built-in e-prescribing functionality | Advanced customization may take extra time to configure initially Certain specialty-specific templates could benefit from deeper optimization |
Best For
The software is designed for family medicine, pediatrics, and primary care, etc.
Key Features
- Medical Billing
- Electronic Prescribing
- Telehealth
Pricing
Pricing for RXNT starts at $118/provider/month for its EHR Bundle. Other than this bundle, the vendor offers the following plans:
- Full Suite – $319/month/provider
- PM Bundle – $207/month/provider
- E-Prescribing – $665/year/provider
Disclaimer: The pricing is subject to change.
Why We Like It
RXNT’s Smart Forms make documentation easier for busy FQHCs. With 2,000+ customizable templates, providers can chart consistently without sacrificing flexibility. This reduces errors, avoids duplicate tests, improves team communication, and supports better patient outcomes, while fitting real-world community health workflows.
User Ratings
Rated 4.1/5 based on numerous user reviews, the software is praised for its user-friendliness. However, some users think that the software should offer merging multiple forms into a single encounter.
6. Meditab
Trusted by community health centers for over 25 years, Meditab addresses the unique administrative and clinical needs of FQHCs. Meditab’s Intelligent Medical Software (IMS) supports clinical documentation, grant tracking, Medicare Prospective Payment workflows, and telemedicine integration in a unified system. Designed for high‑volume, multi‑service environments, the software helps FQHCs streamline operations, automate complex billing and reporting tasks within one reliable interface.
Pros | Cons |
Customizable configurations for various medical specialties Mobile apps enable real-time access to clinical and administrative workflows Patient engagement tools to improve communication | Some specialty templates could be improved Limited customization options for a few advanced features, according to a Meditab EMR review |
Best For
The software is designed for various specialties like ob/gyn, ophthalmology, dental, and mental health.
Key Features
- Patient Scheduler
- Medical Billing
- Telemedicine
- Patient Engagement
Pricing
Meditab pricing plans vary based on the practice size, number of providers, and requirements.
Disclaimer: The pricing is subject to change.
Why We Like It
Meditab’s grant tracking module helps FQHCs efficiently manage all grants in one consolidated system. It simplifies application, monitoring, and reporting processes, reducing administrative workload. Health centers can ensure compliance, maintain accurate records, and free staff to focus more on patient care rather than paperwork.
User Ratings
Meditab is rated 4/5 and users like the software’s easy-to-use nature which helps them in streamlining their workflow. Though some users think that command and data extraction can be improved.
7. Oracle Health
Oracle Health provides a unified platform for clinical, administrative, and analytical workflows tailored to FQHCs. Its EHR and care coordination solutions centralize patient data, streamline population health management, and support operational efficiency. Participation as a Qualified Health Information Network (QHIN) enables secure, standardized data exchange across providers, public health agencies, and payers.
Pros | Cons |
Automates notes for quick access Centralizes records for full views Tracks trends for risk alerts | Trend analysis requires clean inputs Claim tools need periodic reviews |
Best For
Oracle Health is used by hospitals, healthcare providers, public health, life sciences, etc.
Key Features
- Clinical Suite
- Interoperability Console
- Population Health Analytics
- Financial Operations Module
- Reporting Tools
Pricing
Oracle Health uses custom pricing tailored to each organization, with costs varying based on practice size, number of providers, and selected modules.
Disclaimer: The pricing is subject to change.
Why We Like It
Oracle Health allows FQHCs to minimize reliance on multiple third-party systems by providing both EHR and QHIN connectivity from a single platform. Enterprise-grade security ensures patient data remains protected, while the streamlined architecture reduces downtime risks and supports reliable, continuous care.
User Ratings
Supported by feedback from various users, the software is rated 3.5/5. Users love that they can set up appointments quickly within the system. Though some users think that customer support needs to solve issues more efficiently and promptly.
8. Netsmart
Netsmart offers an EHR and care coordination platform built to support FQHCs and community health organizations as they expand clinical services and manage complex care needs. The system unifies patient records across medical, behavioral, and social service domains to improve continuity of care. The software supports flexible documentation, enables multi‑disciplinary care coordination, and ensures compliance with 42 CFR Part 2 and SAMHSA guidelines. Its interoperability capabilities connect care teams and partners, enabling seamless data exchange across service lines.
Pros | Cons |
The platform meets the HIPAA regulatory benchmark Enables patient-physician facility interactions in domestic settings via Home-Care EHR Android app provides for greater EHR accessibility and multi-device operability Round-the-clock e-Ticket and phone assistance | Users report frequent system crashes and glitches The in-depth analytics function needs to be updated |
Best For
Netsmart is used by the public sector, post-acute care, physical therapy, child and family services, CCBHC, geriatrics, and autism.
Key Features
- Electronic Health Records (EHRs)
- On/Offline Integrated Car
- Value-Based Care
- Mobility
- Public Health
- Integrated Case Coordination
Pricing
Netsmart pricing is customized to the organization’s size, number or providers, and required features.
Disclaimer: The pricing is subject to change.
Why We Like It
Netsmart provides scalable EHR solutions that grow with FQHCs as they expand services, such as medication‑assisted treatment (MAT), behavioral health, and grant‑funded programs. The platform supports streamlined reporting for UDS, HEDIS, and grant KPIs, and maintains unified patient records that improve care coordination and operational efficiency. These capabilities help FQHCs meet rising demand and sustain impact over the long term.
User Ratings
The software is rated 3.6/5 based on extensive user feedback. Users appreciate how the dashboard within the software is easy-to-use, and they can find information on one screen. However, some users think that while switching from online to offline, the software sometimes lags a bit.
9. CureMD
CureMD offers a flexible EHR platform designed to meet the needs of FQHCs and community health centers. The system supports clinical documentation, scheduling, telehealth, and billing from a unified interface. Integrated reporting tools help with UDS and quality measures. CureMD also enables care coordination across medical, behavioral, and social services, helping centers run efficiently with limited IT staff.
Pros | Cons |
Streamlines medical information management for healthcare providers Offers customizable templates for personalized documentation Mobile access enables convenient patient care on-the-go Reputation management tools foster patient trust and satisfaction Streamlines revenue cycle management | Initial setup may require training and adjustment Limited customization options for advanced needs Some charting templates could be improved |
Best For
The software is used by public health, oncology, mental health care, cardiology, and dermatology practices.
Key Features
- AI Medical Scribe
- Telehealth
- Practice Management
- CuremD AI
- Medical Billing
Pricing
CureMD offers the following four pricing plans, with custom pricing, starting at $295/provider/month:
- Practice Management
- Electronic Health Records
- Billing Services
- All-in-One (PM + EHR)
Disclaimer: The pricing is subject to change.
Why We Like It
CureMD EHR’s flexible configuration feature stands out as it supports federal funding needs by streamlining FQHC claims, managing denials, and generating reports. Its UDS-focused tools help centers pursue unpaid claims and meet reporting standards efficiently.
User Ratings
Based on extensive user feedback, the software is rated 3.3/5. Users like the customizable templates within the software as they increase efficiency. However, some users think that customer support needs to be more efficient.
When selecting an EHR for FQHCs, decision-makers should focus on platforms with a proven track record in safety-net settings. The system should align with regulatory requirements, support integrated care models, and scale across multiple sites without increasing administrative burden. Long-term vendor support and reporting reliability matter as much as core clinical features.
How To Choose The Right EHR For FQHC
FQHCs operate differently from traditional practices, so EHR selection should reflect that reality. Prioritize systems built to handle visit-based encounters and mixed payer populations, including Medicaid and uninsured patients.
Reporting capabilities deserve close attention, especially support for HRSA, UDS, and quality measures, as manual reporting can overwhelm lean teams. Care coordination tools should support medical, behavioral, dental, and enabling services within a single workflow.
Moreover, population health features also play a critical role, helping leadership track outcomes, managing risk, and planning interventions across communities. Consider operational scalability as well. An EHR should adapt easily as locations, programs, and service lines grow, without requiring heavy IT involvement or costly customization.
What Not To Overlook
- Support for FQHC-specific encounters and visit-based workflows
- Built-in UDS, HRSA, and quality reporting capabilities
- Integrated behavioral health and care coordination tools
- Population health management and risk stratification features
- Readiness for Medicaid and Medicare compliance
- Multi-site management with role-based access controls
- Interoperability with labs, pharmacies, HIEs, and referral partners
Choosing the right EHR for an FQHC comes down to regulatory alignment, visit-based workflows, strong UDS/HRSA reporting, integrated care coordination, and the ability to scale across multiple sites, without adding operational complexity or IT burden.