Best Payroll Software for Healthcare: Top Picks and Key Features [2026]
The healthcare industry faces some of the most complex challenges when running payroll. Every pay run comes with a long list of variables, including 24/7 staffing, overtime rules, shift differentials, on-call pay, and strict compliance requirements.
That complexity makes choosing payroll software harder than it should be. Many payroll tools are built for standard 9-to-5 teams, not for hospitals, clinics, or care providers that operate around the clock. When a system cannot handle those factors, payroll and human resources teams end up fixing errors, tracking down approvals, and stressing about compliance instead of supporting healthcare professionals and patient care.
In this guide, we break down the best payroll software for healthcare organizations, focusing on tools that handle shift-based work, complex pay rules, and healthcare regulations. We compare leading platforms based on how well they support actual healthcare payroll needs, including accurate time tracking, overtime calculations, and compliance support.
What should payroll software do for healthcare staff?
Functionality
Why it matters
Shift-based payroll calculations
Calculates wages correctly across different shift types (nights, weekends, rotating shifts) without manual adjustments
Overtime and pay rule automation
Automates calculations of overtime rules in accordance with applicable regulations, such as state and union rules
Time and attendance tracking
Tracks employee time and prevents timesheet errors to ensure data is accurate for payroll
Shift differentials, on-call, and premium pay support
Supports and calculates different pay types without manual workarounds
Labor compliance engine
Tracks and applies compliance rules, including federal and state labor laws and ACA requirements that impact healthcare payroll and benefits eligibility
Multi-location and multi-role support
Handles multiple roles and pay rates per employee
Audit trails and reporting
Centralizes and stores clear records for audits, disputes, and reviews, especially in regulated environments.
Tax calculation and filing support
Ensures accurate tax withholdings and filings across multiple states/locations
Scheduling and labor forecasting
Aligns staffing levels with demand, provides real-time visibility into labor costs, reduces unplanned overtime, and helps prevent payroll issues before they happen
Employee self-service
Provides staff access to pay stubs, schedules, and other information without increasing HR workload
Customer support and implementation assistance
Helps healthcare teams resolve payroll issues quickly, navigate complex pay rules, and get support during setup and ongoing changes
Top Healthcare Payroll Software Compared
Our Top Five Picks: Quick Summary
Platform
Best for
Why it stands out
Workforce.com
Healthcare teams with complex schedules and pay rules
Built to handle healthcare teams working in shifts, multiple roles, and compliance rules
Paychex Flex
Mid-to-large healthcare organizations
Tax handling and broad HR support
UKG Pro
Large healthcare organizations with strict compliance needs
Payroll and compliance management at scale across large teams
ADP Workforce Now
Healthcare organizations with standardized payroll needs
Consistent payroll framework with tax and compliance support
Dayforce
Enterprise healthcare organizations
A known enterprise platform known for payroll and compliance across large workforces
#1 Workforce.com
Workforce.com is an all-in-one workforce management and payroll platform designed for organizations that rely on hourly staff, including hospitals, clinics, and other healthcare providers. It brings onboarding, scheduling, time tracking, and payroll into a single system, helping healthcare organizations streamline payroll operations while keeping pay accurate as staff move through different shifts, roles, and stages of employment, including new hires.
Healthcare payroll is rarely straightforward. Overtime, shift differentials, staff working multiple roles, and varying compliance rules all affect how employees are paid. Workforce.com is built to handle that complexity by connecting time tracking and scheduling directly to payroll. Because everything lives in one system, payroll is based on what actually happened during each shift, not manual fixes after the fact.
Here are different key features of Workforce.com that support healthcare payroll:
Time and attendance and HR software directly connected to payroll and ensures that timesheets, employee classification, and pay calculations are accurate
Accurate payroll calculations even when staff work nights, weekends, overtime, or variable schedules.
Overtime and pay rule automation to ensure overtime, premium pay, and healthcare-specific pay rules are applied to avoid manual adjustments
Support for multiple roles and pay rates per employee for staff working across departments or roles with different rates
Compliance and audit support that helps standardize payroll workflows and provides clear records for reporting, labor law compliance, audits, and payroll reviews
Labor forecasting to help plan staffing levels in advance and reduce unplanned overtime
Multi-location payroll to consistently support departments, facilities, and locations
Employee self-service with mobile app access for viewing pay stubs, clocking in, managing direct deposit details, requesting time off, and updating personal information.
Pros
- Built to handle complex healthcare schedules and pay rules
- Reduces payroll errors by connecting scheduling, time tracking, and payroll
- Strong labor forecasting to meet staffing ratios and coverage requirements
- Labor compliance guardrails to ensure regulations are adhered to at every stepβfrom scheduling staff to paying them
Cons
- Best value comes from using payroll alongside scheduling and time tracking
- May offer more workforce management functionality than very small practices may require
Best for: Hospitals, clinics, and care providers that manage hourly staff working variable schedules and need payroll to stay accurate as shifts and coverage change
Pricing: Workforce.com provides quote-based pricing tailored to each business. Speak with our team to learn more.
#2 Paychex Flex
Paychex Flex is a cloud-based payroll and HR provider used by many healthcare teams in the US. It offers payroll processing, tax filing, and core HR tools to support straightforward payroll needs and compliance requirements.
Pros
- Payroll and tax filing
- Handles multi-state payroll and reporting
- Familiar platform for finance and HR teams
Cons
- Payroll is less tightly connected to scheduling and time tracking
- Some advanced features are add-ons and can drive up costs
Best for: Healthcare organizations that prefer a familiar, widely used platform for payroll processing and tax compliance across multiple states.
Pricing (as of 2026): Paychex Flex offers Select, Pro, and Enterprise plans, all of which are quote-based. Pricing depends on business size, feature requirements, and add-ons.
Note: Pricing details are based on information available as of 2026. For the most current pricing and features, please refer to Paychex's official website.
#3 UKG Pro
UKG Pro is a human capital management (HCM) platform that offers tools for HR, time and attendance, and workforce management. It's commonly used in large and mid-sized organizations, including healthcare systems.
Pros
- Payroll and HR capabilities
- Employee data and self-service features for managers and staff
- Reporting and analytics
Cons
- Can create a steeper learning curve for users
- Navigation can be less intuitive for users
- Setup generally requires more time than simpler systems
Best for: Mid-sized to large healthcare organizations that need a system with payroll and HR capabilities, and are also prepared to invest in training and setup.
Pricing (as of 2026): Pricing is quote-based and depends on features, modules, and workforce size.
Note: Pricing details are based on information available as of 2026. For the most current pricing and features, please refer to UKG's official website.
#4 ADP Workforce Now
ADP Workforce Now is also a viable choice for healthcare teams' HR and payroll needs. It provides a standardized approach to payroll, tax processing, compliance, and related payroll services. It is a common choice for healthcare providers operating across multiple locations because it can handle regulatory requirements in different states.
Pros
- Payroll and tax handling
- Employee self-service
- Widely adopted and familiar to HR and finance professionals
Cons
- Advanced features often require add-ons
- Learning curve and interface navigation challenges
Best for: Healthcare organizations with multi-state payroll and HR compliance requirements and need a widely adopted platform.
Pricing (as of 2026): Pricing is quote-based and depends on features, modules, and workforce size.
Note: Pricing details are based on information available as of 2026. For the most current pricing and features, please refer to ADP's official website.
#5 Dayforce
Dayforce is a cloud-based payroll and human capital management (HCM) platform often used by healthcare organizations that handle diverse pay rules and operate across multiple locations.
Pros
- Centralized payroll, HR, and benefits
- Support for multiple pay rules
- Employee self-service
Cons
- Reporting can be challenging
- Steep learning curve
- Implementation may require significant training and resources
Best for: Large healthcare teams that deal with complex payroll structures and compliance requirements, and have the capacity to invest in setup and ongoing administration.
Pricing (as of 2026): Pricing is quote-based and depends on features, modules, and workforce size.
Note: Pricing details are based on information available as of 2026. For the most current pricing and features, please refer to Dayforce's official website.
Other Notable Options
These platforms didn't make the top shortlist, but they're still worth considering depending on your business needs.
Gusto
Best for: Small to mid-sized healthcare providers looking for a simple and intuitive payroll and HR solution
Why consider it: Easy and automated payroll system with basic HR tools
Pros: User-friendly with unlimited pay runs, tax filing support, benefits administration, and employee self-service
Cons: May not be as scalable for larger healthcare teams with more advanced needs, and some features may require higher-tier plans
Paylocity
Best for: Mid-sized healthcare teams that need workforce tools alongside payroll
Why consider it: Offers payroll solutions along with talent management tools
Pros: Payroll system that comes with training and credential tracking tools
Cons: May be more complex for smaller clinics, and advanced modules add to implementation time and cost
Viventium
Best for: Healthcare organizations, especially those with a focus on home health, senior care, and similar verticals
Why consider it: Tailored specifically for healthcare providers
Pros: Ease of use and features geared towards healthcare industry requirements
Cons: Limitations with reporting and other customizations
What are the payroll challenges for healthcare organizations?
Payroll in healthcare tends to be more complicated than in other industries due to factors such as round-the-clock operations, strict regulations, and multiple employee types with varying pay rules. Even small payroll mistakes can quickly lead to violations of labor rules, unexpected labor costs, and a poor employee experience for healthcare professionals.
Here are some of the common payroll challenges in healthcare:
24/7 staffing and variable schedules: Healthcare facilities, such as hospitals, clinics, and care providers, typically operate around the clock. Most employees can be scheduled to work nights, weekends, rotating shifts, and on-call hours, making it more challenging to calculate pay, especially when systems are built only for standard schedules.
Overtime, premiums and shift differentials: Healthcare payroll often involves overtime rules, premium pay, and shift differentials that vary by role, location, or labor agreement. Tracking and applying these rules can be time-consuming and error-prone when handled manually.
Employees working multiple roles: It's common for healthcare staff to work across departments or hold multiple roles with different pay rates. It's easy to over- or underpay staff without the right payroll system.
Multi-location and multi-state payroll: Healthcare organizations operating across multiple locations or states need to manage an additional layer of complexity related to tax withholding, reporting, and labor laws, particularly when employees work across facilities.
Gaps between payroll and workforce systems: Using a separate payroll system from time and attendance and employee scheduling often leads to fragmented payroll management and challenges when calculating wages. When these systems don't talk to each other, payroll teams are forced to rely on manual imports, spreadsheets, or last-minute adjustments to reconcile hours worked. This disconnect makes it harder to catch issues before pay runs.
Final Thoughts: Choosing the right payroll software for your healthcare team
For organizations operating around the clock, payroll accuracy depends heavily on how well payroll connects with time tracking, scheduling, and labor forecasting.
While many payroll software solutions support healthcare organizations, not all can handle complex requirements and the nuances of managing healthcare staff. More traditional systems tend to focus on standardized payroll processing and compliance. Meanwhile, enterprise platforms offer deeper control, but that added flexibility can come at the cost of longer setup times.
Workforce.com stands out because it's built around how healthcare teams actually work. It brings together time tracking, scheduling, labor forecasting, and payroll into a single system, enabling healthcare teams to catch issues before pay runs, reduce manual adjustments, and gain better visibility into labor costs. That makes it easier to stay compliant, control overtime, and pay staff accurately.
For healthcare organizations managing variable schedules, multiple roles, and ongoing staffing challenges, Workforce.com offers the most comprehensive and practical payroll solution. It's the strongest option for teams that want payroll to work as part of their workforce operations, supporting healthcare professionals rather than operating as a separate system that only comes into play at the end of the pay period.
See Workforce.com in action today. Book a call with our team to know more.