6 Best Payroll Software for Healthcare (2026)

Healthcare payroll software is designed to automate the payroll management process in the healthcare industry. It facilitates the handling of payroll payments and accounting for various financial aspects related to staff payroll.

Here are some of the main features that are commonly provided by healthcare payroll management software:

• Timekeeping
• Payroll calculation and deductions
• Leave and sick leave management
• Regulatory and legal compliance
• Reporting and analytics.

The choice of HR software is huge.

On the Software Suggest website, a search for "payroll software for healthcare" brings up a list of 140 suggestions.

So how do you choose the right one for you?

We have done some of the work and will tell you about the best deals on workforce management software in English-speaking countries.

Key Healthcare Payroll Challenges and Features to Look For

Finding the best payroll software for healthcare means looking beyond basic paycheck generation. Medical practices deal with highly specialized operational hurdles that standard payroll systems simply cannot handle.

First, healthcare facilities must manage complex compensation structures. This includes processing per diem pay, hourly wages, and net collections for various clinicians. You also need a system that easily calculates shift differential pay to properly compensate nurses and staff who work nights, weekends, or holidays. Standard payroll tools often lack the logic to automate these multi-rate structures.

Another major challenge is compliance and security. Healthcare practices must strictly adhere to HIPAA regulations. Choosing a platform that ensures HIPAA compliance payroll processing is critical to protecting sensitive employee and patient data. Furthermore, your software must help you manage OSHA reporting for workplace safety and track Affordable Care Act (ACA) reporting to avoid hefty IRS penalties.

Finally, medical facilities face unique staffing and compliance hurdles. Modern payroll systems integrate with scheduling software to enforce safe nurse-to-patient ratio limits. They also feature medical staff credentialing tracking. This allows administrators to receive automated alerts before a critical RN license or CPR certification expires, preventing compliance violations and sudden staffing gaps.

Our Methodology: How We Chose the Best Payroll Software for Healthcare

To build this list of the top six recommendations, we evaluated numerous platforms against criteria specifically relevant to medical practices. We selected these tools based on their ability to handle complex pay structures, ensure regulatory compliance, and integrate smoothly with existing healthcare operations.

1. Gusto

Gusto is an HR system, one of the main functions of which is the automation of payroll calculations. For medical practices, Gusto excels at handling complex pay structures, easily allowing administrators to configure rules for shift differential pay, hourly wages, and per diem staff.

The gusto platform allows you to pay your employees as many times a month as necessary. The developers do not charge any additional fees. Gusto automatically fills and files payroll taxes, synchronising the hours of work of the team.

All necessary forms for HR specialists are stored and filled out online:

• I-9;
• W-2;
• Contractor 1099 form;
• Form 941, etc.

To free up time for important tasks, you can activate payroll on AutoPilot using free payroll software. This is an optional feature from Gusto that allows you to payroll automatically at a designated period.

Gusto has its own debit card that allows you to get simplified access to your payroll on a payday. Additionally, Gusto supports HIPAA compliance payroll by securely storing sensitive employee data and offering built-in ACA and OSHA reporting features to keep your practice fully compliant.

The platform offers advanced features as well:

1. Payroll reports are used to analyse bank transfers, payments, and tax deductions.
2. Integration with Receipt Bank.
3. Automatic employee time tracking.
4. Integration with Xero, QuickBooks, and FreshBooks.

Pricing

Gusto offers three pricing plans: Simple, Plus, and Premium.

Prices start at $40 per month plus $6 per user. You might even find a valuable Gusto discount by checking their current offers or signing up for an introductory period, making their comprehensive features even more accessible.

If you run a contractor-only business, Gusto has a separate plan for you with a discounted base price of $0 per month for 6 months and an additional $6 per month per contractor.

2. ADP

This comprehensive payroll solution is widely used by many businesses. It offers services from human resources and payroll to benefits, talent, and compliance. ADP is highly regarded in the medical field because it provides tools specifically designed for HIPAA compliance payroll and robust ACA tracking, ensuring large clinics and small practices alike avoid costly regulatory fines.

ADP has positioned itself as software that can serve both small businesses and corporations with 1000+ employees. You can work either on a computer or in a mobile app.

Key features:

1. Autopilot payroll
2. AI-powered payroll inspector to detect errors in receipts
3. Employee time tracking.
4. Full automation of tax payments.
5. Maintain reporting for tax authorities.
6. Self-service onboarding for employees.

Pricing

ADP does not provide open information about the cost of services on its website. The price of the connection depends on the number of employees and the frequency of pay days and is announced after consultation.

According to some sources, the Essential Plan starts at $79 per month plus $4 per employee.

3. QuickBooks Payroll

This versatile payroll service integrates directly with QuickBooks' extensive accounting software. For healthcare providers, QuickBooks offers automated time tracking that syncs directly with payroll, ensuring accurate payouts for hourly clinical staff, overtime, and complex shift differentials.

The platform offers the following features:

1. Same-day direct deposit. You can enter employee data on hours worked, PTO, or payroll. Salary checks will be automatically deposited on the day you pay salaries.
2. Automated tax payment. Fill out the forms online. The platform will do the rest.
3. Tax penalty protection. If you've received a tax penalty while working with QuickBooks, you'll be paid up to $25,000, which will help you resolve problems with the IRS.
4. Time tracking. You can create schedules, approve time, track employees on shift, and create payroll planning reports.
5. Integrations. QuickBooks supports integrations with ADP, Square, Gusto, Paychex, Dropbox, OnPay, etc.

The platform works with both small businesses (accountants) and medium- to large-sized companies, including healthcare practices.

Pricing

QuickBooks has a total of four pricing plans:

The payroll option is added separately and costs from $22.5 to $62.5 per month, depending on the features and a plan.

For example, in the Essentials plan, the Payroll Core feature costs $22.5 per month and includes automated payroll and taxes, an employee portal, 401(k) plans, 1099 forms, etc. Other options are shown in the screenshot below.

4. Paycor

Known for its excellent customer service and versatile functionality. Paycor is an excellent choice for healthcare practices because it provides robust scheduling integrations that help manage complex clinical shifts, including automated rules for shift differential pay and per diem staff.

The software offers the following features:

1. OnDemand Pay. With Paycor, you can give your employees access to the money they earn before payday. The creators claim that the freedom to dispose of payments attracts and retains more talented people.
2. Mobile Wallet. An app where employees can manage their benefits, request statements, use budget management tools, and direct bill payments.
3. Autorun. Schedule payments in advance and enable automated deferred payments.
4. Tax compliance. In the main menu of the programme, you will be able to see notifications about tax payments and changes in tax legislation.
5. Automatic form filling. Paycor processes forms W-2, 1099, and tax filing.
6. Reports. Payroll reports are generated in two clicks. DDS can analyse cash requirements, tax liabilities, and more.
7. Employee self-service. Employees can access pay stubs on their own at any time with just a mobile phone.

Pricing

Paycor works with businesses of all sizes. The cost is not publicly disclosed and depends on the number of employees in the company. You will need to contact the sales office to confirm the price.

However, the website has information about four tariff plans:

The Capterra website states that the plans start at $99 per month.

5. Staffology Payroll by IRIS

Offers full-featured cloud payroll and an API for businesses and bureaus. This platform is highly adaptable, making it a strong option for practices that need to connect their payroll directly to custom timekeeping or medical staff scheduling software.

Saffology offers its customers a set of features, including:

1. Payroll automation. It includes autopilot abilities, payslip distribution, payments summary, and automated timesheets.
2. API. You can push it into any type of software: accounting, practice management, attendance. Applications that can be integrated include Sage, Xero, Nest, CIPHR, and others. The API is fully open and easily configured for various third-party HR platforms.
3. Accounting integration. After salaries are paid, it's time for accounting. Staffology integrates with KashFlow, Reckon One, AccountsIQ, QuickBooks, and others, so you can automatically create journal entries.
4. Compliance and Automation. The platform is built to handle automated tax filings and compliance reporting seamlessly. It easily adapts to different state and federal tax structures to keep multi-location practices compliant.
5. Reports. Create detailed operational and payroll reports to analyse your business and tax liabilities without leaving the platform.

Pricing

The cost of an additional employee depends on the number of payslips created each month. The more employees, the lower the cost of additional payslips.

The pricing is entirely custom and scalable based on your practice's needs. You can use the handy calculator on their website to determine the cost of a subscription based on your specific number of employees and required API integrations.

Please note, it is essential to choose the payroll software that best suits your business's specific needs. Each software solution listed offers a diverse range of features and tools that best serve different types of businesses.

Practice Management Software with Payroll Software Options

Direct payroll functionality may not be a standout feature of most medical practice management software. However, they usually provide compatibility or integration capabilities with other payroll processing tools, thereby seamlessly incorporating payroll functions into the system.

For many healthcare providers, the choice of a PMS with an additional payroll module will be preferable. For the same amount of money, they get more functionality for many HR tasks at once:

• Health records management.
• Optimised appointment booking.
• In-depth analytics of all aspects of the institution's work.
• The possibility of remote work, and much more.

To streamline these processes, adopting an end-to-end HR platform can further enhance efficiency by centralizing all HR software solutions, including payroll, in one unified system.

Consider pairing your practice management system with contract management software to streamline both payroll and contract-related tasks efficiently.

We will also tell you about PMS and the quality HR solutions inside.

6. Medesk

This practice management software provides professional HR tools for patient interaction, payrolls, and patient billing.

Medesk is uniquely designed for healthcare practices, offering built-in medical staff credentialing tracking to ensure no critical licenses expire unnoticed. It also integrates seamlessly with scheduling systems to maintain proper nurse-to-patient ratio limits across all shifts.

Medesk automatically tracks doctors' working hours, generates reports on amounts paid and days worked. Within the platform, you can split payments into fixed and bonus payments, create a reward system for clinicians and admin staff.

Medesk bonus calculations help you build a transparent system of rewards based on different parameters and the achievements of your employees:

• bonuses for performed appointments, paid invoices;
• different percentages of bonuses for different services rendered;
• bonuses to the receptionist for the number of booked appointments and absence of no-shows.

We recommend using the analytics module reports to identify employee experiences worthy of reward and to strengthen your human capital management.

Pricing

Medesk offers a permanent Free plan (available in every market) and a paid Pro plan.

The payroll feature is available on the Pro plan for $28/month for 30+ features that cover all the needs of healthcare professionals.

The Importance of Time-Tracking and Scheduling Integrations

In a healthcare setting, payroll is deeply tied to staff scheduling. Advanced time-tracking integrations do more than just clock employees in and out. They actively enforce legal staffing limits, such as maintaining a safe nurse-to-patient ratio during busy shifts.

Furthermore, these integrations manage license-based shift assignments. By integrating your scheduling software with your payroll system, you ensure that only properly certified staff members are assigned to specific medical shifts. This prevents compliance issues and guarantees that complex clinical pay, like per diem rates and net collections, is calculated accurately based on the exact hours and roles worked.

How to Choose the Best Payroll Software for Healthcare

Selecting the best payroll software for healthcare requires more than comparing price tags. Healthcare organisations face unique challenges: managing shift differentials, tracking certifications, maintaining compliance with constantly changing labour regulations, and handling complex pay structures for clinical and administrative staff alike.

Here are the key factors to evaluate before committing to a platform:

Taking the time to assess these factors against your organisation's specific setup will save significant time and cost in the long run.

Frequently Asked Questions

What does healthcare payroll software do? Healthcare payroll software automates compensation for medical staff while ensuring compliance with industry regulations. It handles complex pay structures like per diem, hourly, and net collections. Additionally, it integrates with scheduling tools to manage overtime and track clinical shift differentials accurately.

How does payroll software handle complex clinical pay? The software allows administrators to set custom pay rules for different roles and shifts. It automatically calculates varying rates for per diem work, night shifts, and weekend differentials. This ensures that clinicians and nurses are paid accurately without requiring manual calculations.

How do these systems manage compliance? Healthcare payroll platforms include built-in compliance features for HIPAA, ACA, and OSHA regulations. They securely store employee data to maintain privacy. The software also tracks medical staff credentialing by sending automated alerts before licenses or certifications expire.

Summing Up

Choosing the right healthcare payroll software is crucial if you want to streamline operations and ensure compliance within the healthcare sector. Making the right choice demands careful consideration of the specific needs and requirements of your organisation.

1. Among the top contenders in the market, Gusto stands out for its user-friendly interface, automated payroll processing, and integration capabilities with popular accounting software.
2. Meanwhile, ADP offers a comprehensive suite of services catering to businesses of all sizes, with features such as autopilot payroll and AI-powered error detection.
3. QuickBooks Payroll provides seamless integration with its accounting software, along with same-day direct deposit and automated tax payments.
4. Paycor offers innovative features like OnDemand Pay and a mobile wallet, ensuring flexibility and convenience for employees.
5. If you are seeking a highly adaptable solution, Staffology Payroll by IRIS offers cloud-based payroll automation, robust API integration, and custom compliance options for growing practices.
6. Medesk stands out for its robust practice management tools, including advanced payroll features such as bonus calculations and comprehensive analytics.

The choice between a standalone payroll system and practice management systems with integrated payroll functionality depends on the unique needs and priorities of your healthcare organization.

You can find a detailed review of the top PMS on the market in our blog. We're analysing our competitors to help you make a thoughtful choice that will improve overall patient care.