Managing payroll in healthcare demands a lot more than issuing paychecks twice a month. It goes without saying, the process is complex, as it requires dealing with various regulatory authorities depending on where your practice is located.

What makes it worse? Payroll errors. Often a result of manual processing, these issues frustrate employees, besides affecting the quality of care patients receive. And that is where dedicated healthcare payroll software fits in. With features tailored to the healthcare industry, these platforms automate the entire process, leaving little to no room for errors and discrepancies.

This in-depth guide covers the top 9 payroll software tailored to meet the requirements of the healthcare industry.

9 Best Payroll Software For Healthcare: At A Glance

Software

Our Rating

Features

Pricing

Viventium 

4.1

  • Applicant tracking
  • Onboarding
  • Scheduling and time

Custom pricing

Paylocity

4.3

  • Improve time allocation
  • Simplify payroll
  • Train and certify

Custom pricing

Netchex

5

  • Learning management
  • Performance management
  • Employee self-service portals

Custom pricing

Paycor

4.3

  • Healthcare workforce analytics
  • Scheduling integration
  • Compliance management tools

Custom pricing

Paycom

4.6

  • Vault
  • Everyday®
  • Paycom Pay®

Price ranges from $25-$36/employee/month

Workday HCM

4.1

  • AI-Powered healthcare insights
  • Financial system integration
  • Global compliance management

Custom pricing

ADP RUN

5

  • Retain skilled staff
  • Exceptional employee experience
  • Simplify compliance

Custom pricing

Gusto

4.4

  • Automate and streamline operations
  • Ensure compliance for your practice
  • Attract and retain your dream team

Pricing starts at $49/month

Rippling

4.9

  • Powerful reporting tools
  • Scheduling
  • Onboarding automation

Pricing starts at $8/user/month

1. Viventium – Best For Healthcare-Specific Payroll Management

Vivintium helps healthcare organizations stay compliant and connected while operating efficiently through its advanced feature set. The platform optimizes the payroll process for medical centers through flexible and user-friendly software. It is designed for long-term use in care homes, hospices, senior, and skilled care settings.

This software provides an all-in-one workforce solution. It includes CMS-compliant PBJ reporting, paperless onboarding, AMS/EHR integrations, licensing tracking, and on-demand payment functionality. With these tools in place, healthcare organizations can better manage their staff and control labor costs.

Key Features

  • Applicant Tracking: This feature helps automate candidate management, interview scheduling, and credential verification tools to streamline the healthcare hiring process
  • Onboarding: The onboarding platform eases the process and prepares the new employees from day one
  • Scheduling And Time: You can manage shifts, overtime, and time-off requests easily with these smart scheduling tools for every department and location

Pricing

Viventium provides personalized pricing based on your organization’s needs.

Disclaimer: The pricing is subject to change.

Pros And Cons

Pros:

  • It has a helpful and accessible reporting
  • Support staff are consistently helpful in answering questions
  • Easy to navigate for both administrators and employees

Cons:

  • No direct employee messaging feature in the ESS portal
  • Account setup requires extra effort at the beginning

2. Paylocity – Best For All-in-One Healthcare HR And Payroll

Paylocity HR & Payroll is a complete HR and payroll solution built for healthcare. It helps reduce administrative burden and error, particularly in an environment with variable shifts, overtime rules, and strict regulatory requirements. Its scheduling tools highlight staffing gaps and allow staff to claim or swap shifts via mobile, while its compliance dashboards monitor things like Fair Labor Standards Act (FLSA), break rules, and credential expirations.

For healthcare providers, the platform delivers tangible benefits. For instance, it provides workforce analytics to monitor turnover, overtime costs, and retention trends that help in better workforce decisions. Having said that, Paylocity works as a tailored solution for managing the payroll and challenges of an industry defined by regulations and round-the-clock operations

Key Features

  • Improve Time Allocation: With advanced scheduling tools, you can stay on top of shifts, reduce missed workdays, keep track of tardiness, and manage shift differentials across your team
  • Simplify Payroll: The platform lets you go fully paperless by handling payroll and compensation digitally
  • Train And Certify: A built-in training and certification system keeps employee credentials organized and compliance requirements easy to track

Pricing

Paylocity structures its pricing around three modules: HR, Finance, and IT. Payroll is bundled within the HR module and is billed at a custom rate.

Disclaimer: The pricing is subject to change.

Pros And Cons

Pros:

  • Automated payroll processing with built-in compliance
  • Employee self-service portal for easy access
  • Integrated time tracking and talent tools

Cons:

  • Mobile app lacks advanced features
  • Reporting capabilities need improvement

3. Netchex – Best For Healthcare Compliance Management

Netchex is a cloud-based Human Capital Management (HCM) platform that brings payroll, HR, benefits, and employee management into one system. Designed for growing businesses across industries, including healthcare, it streamlines staff payments, scheduling, and compliance management in a single, easy-to-use solution.

What makes Netchex stand out is its balance of simplicity and depth. Businesses value its intuitive design alongside powerful automation and reporting. This reduces administrative workload and gives leaders more time to focus on people and strategy instead of manual tasks.

Key Features

  • Learning Management: With this feature, healthcare staff can get access to training programs, keep up with continuing education, and stay on top of their certifications
  • Performance Management: This tool makes it easier to handle reviews, set goals, and track progress for employees across different roles
  • Employee Self-Service Portals: These portals give staff a way to check schedules, request time off, view their pay, and manage benefits from their devices

Pricing

Netchex offers custom pricing based on organization size and required features. These include:

  • Core
  • All-In
  • Flex

Disclaimer: The pricing is subject to change.

Pros And Cons

Pros:

  • Clear and detailed payroll reports
  • Strong and well-handled implementation tools
  • Intuitive interface with easy navigation

Cons:

  • Staff can update details independently
  • Insurance benefits integration feels limited

4. Paycor – Best For Healthcare Workforce Analytics

Paycor software is a cloud-based payroll and HR platform. It helps healthcare organizations manage complex workforce needs. These include shift-based scheduling, time tracking, and payroll compliance. It automates payroll processing, tax filing, and benefits administration, while also offering employee self-service tools so staff can access pay stubs, schedules, and time-off requests anytime, anywhere.

Since Paycor streamlines workforce management while keeping compliance at the forefront, it’s a great choice for healthcare providers. Its scheduling, reporting, and payroll features reduce administrative work, and its mobile access ensures ease for staff.

Key Features

  • OnDemand Pay (EWA): This feature lets employees get the money they’ve already earned anytime they need it. It also gives them tools like budgeting help and free financial advice to better manage their finances
  • Scheduling: Managers can copy and move shifts across days or weeks to ensure the right nurses with the right certifications are always scheduled
  • Reporting + Compliance: Using it, employers can easily complete and review federal and state forms like I‑9s and W‑4s online. It also supports long‑term care providers by handling PBJ reporting

Pricing

Paycor offers the following pricing plans:

Below 50 Employees

  • Basic
  • Essential
  • Core
  • Complete + ASO

It also offers a custom pricing plan for organizations with 50+ employees, which includes a one-month trial.

Disclaimer: The pricing is subject to change.

H3> Pros And Cons 

Pros:

  • Intuitive interface with all-in-one HR tools
  • Automated payroll with accurate tax calculations
  • Robust reporting tools

Cons:

  • Mobile app lacks full desktop functionality
  • Setup and module navigation can be complex

5. Paycom – Best For Employee Self-Service Healthcare Payroll

Paycom sets itself apart in the healthcare payroll field through its strong focus on security, automation, and compliance. Recognized as an American Hospital Association’s Preferred Cybersecurity Provider Program, Paycom gives healthcare organizations confidence in protecting sensitive employee and patient data.

Unlike many systems, Paycom uses a single-database architecture, ensuring all payroll, HR, scheduling, and compliance data flows without duplication or errors. Its standout tool, Beti®, allows employees to verify and correct their own payroll information before submission.

The software deals with scheduling, compensation schemes, and compliance requirements across various departments and across geographic locations.

Key Features

  • Vault: It is a Visa®-based payroll card option that lets employees have part or all of their wages loaded onto a digital/payroll card instead of a traditional paper check
  • Everyday®: This feature lets employees get paid daily by depositing earned wages onto their Vault Visa® Payroll Card instead of waiting for the usual payday
  • Paycom Pay®: Paycom Pay issues paychecks from its own account, so you don’t have to reconcile dozens of individual checks from yours

Pricing

The vendor’s pricing depends on business needs and typically ranges from $25 to $36/employee/month.

Disclaimer: The pricing has been sourced from third-party websites and is subject to change.

Pros And Cons

Pros:

  • Employee self-service for personal management
  • Automated payroll with multi-jurisdiction compliance
  • Real-time analytics for workforce decisions

Cons:

  • Limited interface and workflow customization
  • Scheduling tools may feel basic for more complex needs

6. Workday HCM – Best For Enterprise Healthcare Organizations

Workday HCM provides a payroll system as a part of its broader HCM suite. It automates calculations, deductions, and tax filings while integrating directly with HR and time-tracking data. For healthcare providers, this means payroll updates (overtime, shift differentials, or benefits changes) flow automatically.

What makes it stand out is its real-time recalculation and flexibility, where any pay or benefits changes reflect instantly without batch processing. As payroll data connects with finance, HR, and scheduling in one system, managers can clearly see the financial impact of staffing decisions across units or departments.

Key Features

  • Payroll Management: This feature automates complex payroll tasks to reduce manual tasks
  • Global Payroll Integration: It lets healthcare organizations manage payroll across locations to ensure compliance in multiple regions
  • Reporting And Analytics: It gives healthcare leaders real-time insights into workforce costs for smarter staffing and budget decisions

Pricing

Workday offers custom pricing tailored to each organization’s size, needs, and chosen modules.

Disclaimer: The pricing is subject to change.

Pros And Cons

Pros:

  • User-friendly across desktop and mobile for all roles
  • Guided support for complex workflows
  • End-to-end recruitment with employee self-service

Cons:

  • Limited customization of interface layout
  • Inconsistent updates on applications and pay range

7. ADP RUN – Best For Multi-Location Healthcare Organizations

RUN Powered By ADP is a cloud-based payroll and HR platform built to automate tasks such as wage calculation, tax filing, and benefit deductions. It integrates with time and attendance systems so that hours worked flow directly into payroll. This is especially helpful in healthcare, where staff often work variable shifts, overtime, or on-call hours.

Its compliance support and adaptability for organizations with multiple locations and regulatory requirements make it stand out. The software’s automatic updates and alerts help payroll teams stay aligned with current regulations. This is particularly true for healthcare, where labor laws, tax rules, and benefit structures can vary widely.

Key Features

  • Compensation Management: It lets healthcare organizations handle different pay structures, including multiple pay rates and shift differentials
  • Integrated Payroll Control: It combines payroll with time and attendance tracking, plus direct deposit or mobile payroll
  • Personalized Payment Options: This gives employees flexibility in how they receive pay, including paperless options through Wisely®

Pricing

The vendor offers multiple pricing plans, with a 3-month free payroll trial. The plans include:

  • Essential Payroll
  • Enhanced Payroll
  • Complete Payroll & HR+
  • HR Pro Payroll & HR

Disclaimer: The pricing is subject to change.

Pros And Cons

Pros:

  • Accessible support ensures smooth operations
  • User-friendly payroll tools with mobile access
  • Employee self-service portal for pay, tax, and personal data access

Cons:

  • Limited customization options available
  • Reporting capabilities could be improved

8. Gusto – Best For Small To Mid-Size Healthcare Practices

Gusto offers payroll, benefits, and HR in one cloud-based solution, built with small to mid-size organizations in mind. It handles payroll processing across multiple pay schedules, supports both hourly and salaried staff, and lets employers set up multiple pay rates or off-cycle payrolls.

It also automatically calculates, files, and remits all relevant federal, state, and local payroll taxes. For healthcare settings, this means it can deal with things like per-diem staff, shift premiums, and syncing hours from time-tracking tools so payroll reflects actual worked time with fewer manual corrections.

Key Features

  • Payroll Taxes: Gusto calculates and files payroll taxes for you with the correct government agencies every payroll cycle, included at no extra cost
  • Instant and Same-Day Pay: It offers 24/7 payroll processing so employees can get paid instantly or the same day
  • Pay-As-You-Go Workers’ Compensation: It lets you set up and manage workers’ compensation online, paying premiums gradually instead of in one large lump sum

Pricing

The platform offers three pricing plans, covering payroll, HR, and benefits in one place. These include:

  • Simple: $49/month + $6/user/month
  • Plus: $80/month + $12/user/month
  • Premium: $180/month + $22/user/month

Disclaimer: The pricing is subject to change.

Pros And Cons

Pros:

  • Supports domestic and international contractor payroll
  • Offers charitable giving and college savings benefits
  • Provides tax filing and financial wellness tools

Cons:

  • No built-in invoicing or receivables tools
  • Requires extensive manual data entry upfront

9. Rippling HR – Best For Healthcare Organizations Seeking Complete Workforce Management

Rippling HR is part of Rippling’s unified platform that ties HR, IT, benefits, and finance data together in a single system. Hence, payroll draws from a ‘single source of truth’ for employee information rather than siloed spreadsheets.

Because it’s tightly linked with time-tracking, benefits, and HR modules, any changes in roles, hours, or compensation immediately reflect in payroll without needing separate imports.

These connected models help reduce errors when staff move between units, take shifts in different specialties, or adjust work hours, since all upstream HR and scheduling changes flow into payroll continuously.

Key Features

  • Employer of Record (EOR): This service offers legal handling and compliance aspects of employment for healthcare organizations. This way, providers can expand their workforce internationally without the need to establish local entities
  • Contractor Of Record: This service handles compliance, payments, and tax reporting for healthcare organizations, so contractors are properly classified and paid on time
  • Global Payroll Service: Using this service, you can pay employees in multiple countries, in local currencies, while ensuring compliance with local laws

Pricing

Rippling offers modular pricing, starting at $8/user/month, with an additional $40 monthly base fee.

  • Rippling Platform
  • Rippling HCM
  • Rippling IT
  • Rippling Spend

Disclaimer: The pricing is subject to change.

Pros And Cons

Pros:

  • Convenient calendar sync with personal schedules
  • Streamlines access for teams in multiple offices and remote roles by securely centralizing logins
  • Fast setup with adaptable options for varied business needs

Cons:

  • Spend‑Intacct sync misses bill details
  • PTO calendar export lacks shared view and updates

Choosing The Best Payroll Software For Healthcare

As healthcare organizations grow, handling payroll can get complicated with shift work, compliance rules, and large teams. The right payroll software makes this easier by automating tasks, reducing errors, and ensuring compliance. When choosing, focus on tools that are simple to use, flexible, and able to grow with your needs.

Each of the options we’ve listed has features built for healthcare. Explore them to find the payroll solution that saves time, reduces stress, and lets you focus more on patient care.