You’re a practice administrator at a busy outpatient clinic, closing out payroll, when you notice two timecards don’t add up. One medical assistant logged hours on the wrong sheet, and another forgot to clock in entirely.
To keep payroll moving, you have to piece together their shifts from memory and patient records — a frustrating process that not only leaves room for error but also takes hours away from patient care. You don’t like it and neither does your staff.
This is just one of many challenges you may face in healthcare. But the problem with these specific challenges is they’re rarely fixed at the source, i.e. your approach to time and attendance.
Specifically in non-hospital settings like private practices, urgent care centers, and rehab facilities, recording hours is just the start of time and attendance. You’re also trying to ensure accurate pay, manage compliance, and control labor costs. Time and attendance touch every part of that.
We’ve mapped out nine of the most common healthcare time and attendance challenges practice administrators face in 2025. We’ll show you how those challenges play out differently, whether you’re a small, mid-sized, or enterprise healthcare organization, and why it’s important to solve these challenges at the source.
Challenge 1: Overtime management and labor costs
When staff shortages or high patient demand go unchecked, overtime becomes the default solution. But unplanned overtime pay quickly drains budgets and fuels burnout, becoming one of the most financially impact healthcare time and attendance challenges.
Take a mid-sized urgent care practice during the holidays — nurses may regularly work beyond 50 hours a week before administrators even realize it. Because their system doesn’t flag approaching overtime thresholds, the costs are already locked in when payroll comes due.
How overtime management impacts time and attendance by organization size
SMB: Small teams often can’t avoid overtime because staff is lean, but every additional hour strains already tight budgets.
Mid-market: Overtime slips through when each clinic tracks hours in isolation, leaving administrators with incomplete data.
Enterprise: Reporting systems exist, but fragmented data across regions delays intervention and increases costs.
Challenge 2: Compliance with labor laws and union rules
Few healthcare time and attendance challenges weigh heavier on healthcare administrators than compliance with Fair Labor Standards Act (FLSA), state laws, and Collective Bargaining Agreements (CBAs).
A rehab clinic in California learned this the hard way when staff breaks were logged manually but without timestamps, resulting in state penalties despite employees insisting they had taken them.
How compliance impacts time and attendance by organization size
SMB: Practices struggle to stay up to date with state laws.
Mid-market: Compliance is compounded by union contracts layered on top of state laws.
Enterprise: Managing federal, state, and union rules across regions requires full-time oversight — manual systems simply can’t keep pace.
Challenge 3: Multiple roles and shift differentials
Many staff in outpatient and specialty care wear multiple hats. This complexity shows up quickly as one of the top healthcare time and attendance challenges.
A respiratory therapist might cover a night shift one week and a daytime shift the next, with shift differential pay for each. But errors occur when systems don’t recognize role-based or shift-based pay rules. Staff end up underpaid (and irritated), compliance gaps open, and administrators are left scrambling to correct payroll afterward.
How multiple roles and differentials impact time and attendance by organization size
SMB: Often lack the automation needed to track multiple pay codes.
Mid-market: As roles diversify, the risk of errors increases without automated pay rules.
Enterprise: High volumes of multi-role staff magnify payroll risks — even a small systemic error can ripple across hundreds of paychecks.
Challenge 4: Role-based restrictions
Assigning staff to shifts without verifying credentials can create both compliance and patient safety risks.
Consider a clinic nurse who picks up a shift in a unit where their credentials don’t apply. By the time the issue is discovered, the shift is already underway, and the nursing supervisor is forced to reassign on the fly. These errors disrupt patient care, create unnecessary admin intervention, and expose clinics to liability.
How role-based restrictions impact time and attendance by organization size
SMB: Credential checks often happen manually, which leaves room for mistakes.
Mid-market: Systems may exist but aren’t always integrated with time and attendance solutions.
Enterprise: Credential management is essential at scale, where a single oversight can put entire departments at risk.
Challenge 5: Time theft and buddy punching
Inaccurate time capture is one of the most common and costly healthcare time and attendance challenges.
A receptionist was supposed to start their shift at 7 a.m., but they arrived at 7:07, 7:00, 7:02, 7:13, and 7:08 during the week. However, payroll still credits them with a full shift despite not accounting for the extra 30 minutes. While unintentional, it’s time theft and those minutes add up quickly.
When evaluating healthcare time and attendance challenges that directly impact your bottom line, time theft is one of the most prominent.
How time theft impacts time and attendance by organization size
SMB: Outdated paper or punch clocks make clinics highly vulnerable to inflated hours.
Mid-market: Fraud and unintentional time theft occur across multiple sites without unified oversight.
Enterprise: Financial losses are larger in scale, even with small percentages of fraud, though the right time and attendance solution eliminates the risk.
Challenge 6: Managing distributed locations and mobile staff
Tracking employees and their clock-ins across multiple sites or mobile staff (home health, hospice) is one of the top logistics-focused healthcare time and attendance challenges.
A home health aide might clock in from her phone before leaving home, but not arrive at the patient’s residence for 20 minutes. If a clinic pays for travel time, that gap should be captured. If it reimburses mileage only, the discrepancy needs to be flagged. Rarely are either instances properly documented.
Without location-based tracking (like geofencing), administrators are left sorting through inconsistent policies and incomplete data.
How distributed staff impacts time and attendance by organization size
SMB: Single-site practices are less affected, but policy inconsistencies grow as soon as satellite locations are added.
Mid-market: Multiple sites highlight the difficulty of enforcing travel and reimbursement policies without centralized oversight.
Enterprise: Wide geographic footprints bring a mix of rules and reimbursement policies that require automated enforcement.
Challenge 7: Leave and PTO tracking
When time off requests and PTO accruals are managed in time tracking spreadsheets or sticky notes, errors are inevitable. The manual effort to request time off — texting, calling, taking notes, logging in spreadsheets — eats up worker hours and opens the door to mistakes with accruals, carryover, or approvals.
For example, a dental hygienist who believes she has three PTO days left may find her request denied because the front desk’s manual tracker is outdated. Not only does this create frustration for her, but in some states, it opens the practice to compliance risk if PTO laws aren’t followed.
This is where healthcare time and attendance challenges become full-scale employee engagement challenges.
How PTO and leave tracking impact time and attendance by organization size
SMB: Manual time tracking spreadsheets are the norm, but prone to error and easily outdated.
Mid-market: Multiple managers approving requests without visibility creates inconsistency and disputes.
Enterprise: Complex accrual policies across states and CBAs make manual leave management and PTO tracking impossible to scale.
Challenge 8: Speed, transparency, and accuracy
For staff, knowing their paychecks will be correct and on time is the most essential expectation. But delays creep in when approvals, corrections, and reimbursements are handled manually. Failing with these intangibles is one of the sneakiest healthcare time and attendance challenges.
For example, a front desk admin clocks 10 hours with a skipped meal break for a busy Monday shift. Without automated time tracking and approvals, it’s unclear whether that break counts toward overtime. Meanwhile, a home health aide finishes visits but struggles to get travel time approved for weekly reimbursements.
Your staff need to clearly understand how their hours, overtime, and breaks translate into pay. When systems lack transparency, staff lose confidence and administrators burn extra hours with corrections and manual payroll processing.
How transparency challenges impact time and attendance by organization size
SMB: Rely on manual or basic tools, where even minor delays or lack of clarity cause outsized frustration for staff.
Mid-market: Partial integrations ease the workload, but gaps in visibility (like missed overtime or unclear reimbursements) still make payroll a pain.
Enterprise: Accuracy at scale is non-negotiable — small breakdowns quickly erode efficiency and trust.
Challenge 9: Employee morale and trust in payroll accuracy
Almost all healthcare time and attendance challenges will impact how staff trust (or don’t trust) your practice.
A nurse who experiences two consecutive payroll errors may decide to look elsewhere for employment, adding turnover to an administrator’s list of problems. Payroll mistakes and opaque processes send a clear message to staff: their time isn’t valued.
In a competitive hiring market, that perception can be devastating.
How morale challenges impact time and attendance by organization size
SMB: Errors stem from manual systems and create visible frustration among staff.
Mid-market: Errors compound when spread across sites and roles.
Enterprise: Large-scale payroll errors can lead to public backlash, lawsuits, or union disputes.
How to begin solving healthcare time and attendance challenges
As with any system-first error, the first step in solving your healthcare time and attendance challenges is to understand where the gaps are.
Visibility in time and attendance
Start with visibility by implementing centralized, real-time time tracking across your practice. Without it, you’re left piecing together hours from memory or patient records, as in the payroll scramble we outlined earlier.
A unified system lets you see who’s clocked in, who’s approaching overtime pay thresholds, and which roles are currently staffed. You can fill callouts without burning hours on manual phone trees and never sweat whether or not your employees are getting accurate pay.
Program systems for compliance
Manual time tracking is one of the easiest vulnerabilities to fix in labor compliance.
With the right system, break rules and credential checks are built in. If an assistant forgets to clock out for lunch, the system prompts a correction. If a float pool nurse picks up a shift outside not within their credentials, it’s flagged before they ever step on site.
These safeguards prevent errors, protect patient safety, and shield your practice from costly penalties.
Lean on automation
Automation takes the edge off payroll complexities like shift differentials or travel reimbursement. Instead of administrators manually adjusting pay for a respiratory therapist who covered a night shift, or a hospice aide who logged mileage, the system applies those rules consistently.
Fewer disputes. Fewer corrections. More trust in payroll.
Quick-start roadmap for healthcare time and attendance challenges
☑ Audit processes for accuracy gaps — especially in PTO tracking, shift differentials, and mobile staff policies.
☑ Prioritize integration of time and attendance, payroll, and HR so data flows seamlessly without duplicate entry.
☑ Introduce mobile and biometric options for secure, real-time tracking that reduce errors and buddy punching.
☑ Build compliance rules into your time tracking system, from overtime thresholds to credential expiration alerts.
☑ Train managers and staff on how to use the tools effectively, so the solutions and processes stick.
Turning healthcare time and attendance challenges into strategic advantages
With the right solutions, your healthcare time and attendance challenges go from clerical burdens to true operational strengths.
Real-time dashboards let you spot overtime before it spirals, fill callouts with qualified staff, and ensure shift differentials or credentials are applied automatically. That consistency builds trust with staff, keeps you confident in accurate time for payroll and compliance, and frees administrators from constant rework.
Whether you’re an HR manager, payroll administrator, or clinical director, time and attendance solutions help you get ahead of the daily chaos — because you should be focusing your energy on patients, not fixing timecards.
TCP Software’s employee scheduling and time and attendance solutions have the flexibility and scalability to suit your business and your employees, now and as you grow.
From TimeClock Plus, which automates even the most complex payroll calculations and leave management requests, to Humanity Schedule for dynamic employee scheduling that saves you time and money, we have everything you need to meet your organization’s needs, no matter how unique. Plus, with Aladtec, we offer 24/7 public safety scheduling solutions for your hometown heroes.
Ready to learn how TCP Software takes the pain out of employee scheduling and time tracking? Speak with an expert today.
