Compare payroll software built for hourly employees and time-based pay. Top picks for time tracking integration, overtime calculation, and straightforward hourly payroll.
Hourly employees need accurate hours, correct overtime, and pay stubs that reflect time worked. The best payroll tools integrate with time tracking or include it, calculate overtime automatically, and handle multiple pay rates and schedules without extra hassle.
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Our top payroll picks for hourly employees.
Best overall for hourly payroll4.8From $49/mo + $6/personPayroll with built-in time tracking and automatic overtime. Import hours from Gusto Time or integrate with other time apps. Handles hourly rates, overtime rules, and PTO—all in one platform.
Best for QuickBooks + time tracking4.6From $50/mo + $7/personRun hourly payroll inside QuickBooks with optional QuickBooks Time (formerly TSheets) integration. Labor cost flows into job costing. Good for teams that track time by job or project.
Best value for hourly teams4.5From $49/mo + $6/personHourly payroll with overtime calculation and time-tracking integrations. Flat pricing and one plan. Add your preferred time clock or use OnPay’s options—support included.
Side-by-side at a glance.
| Software | Best for | Starting price | Payroll types | Standout feature | Review |
|---|---|---|---|---|---|
| Gusto | Best overall for hourly payroll | $49/mo + $6/person | W-2, 1099 | Built-in time tracking; automatic overtime | Read review |
| QuickBooks Payroll | QuickBooks + time by job | $50/mo + $7/person | W-2, 1099 | QuickBooks Time integration; job costing | Read review |
| OnPay | Best value for hourly teams | $49/mo + $6/person | W-2, 1099 | Overtime; time-tracking integrations | Read review |
What to look for when you're choosing payroll as hourly employees.
Hourly payroll depends on accurate hours. Look for built-in time tracking (e.g. Gusto Time) or strong integrations with time clocks and apps. Some providers charge extra for time tracking—confirm what's included. Hours should flow into payroll with minimal manual entry.
Federal and state overtime rules (e.g. time-and-a-half after 40 hours) must be applied correctly. The best payroll tools calculate overtime automatically from imported or entered hours. Verify that your provider supports your state’s rules and any industry-specific requirements.
If employees have different hourly rates, shift differentials, or multiple pay types, choose software that supports them without workarounds. Running payroll should be straightforward even with varied schedules and rates.
Many hourly teams track PTO (vacation, sick). Some payroll systems include PTO accrual and use; others integrate with HR or time tools. Confirm how PTO is tracked and how it affects pay when employees take time off.
How each pick fits hourly employees.
Gusto is capable payroll software for hourly workforces that need built-in time collection, automatic overtime rules, and multiple pay rates without bolting on five separate vendors. Hours can flow from Gusto Time or supported clocks straight into approvals and payroll. During your first two payroll runs, import or enter a week with split shifts, meal breaks, and hours over 40 to confirm federal overtime and your state’s daily or seventh-day rules fire correctly. Add PTO requests that cross pay periods to see accruals reduce net pay the way your handbook promises. If you pay different rates by department or location, run a blended schedule and verify each hour lands on the right earning line. When deposits and registers look sane, you have a template for busy seasons.
QuickBooks Payroll is payroll software hourly teams choose when QuickBooks Time (or another integrated tracker) already captures clock-ins by job, customer, or class, and labor must post for costing as well as paychecks. Approved hours should cross into payroll without CSV fixes the night before payday. On trial payrolls, sync a week that includes travel between sites, overtime after inventory, and at least two pay rates to confirm QuickBooks maps burden to the correct jobs or classes. Reconcile the resulting payroll journal to your labor accounts and verify employer taxes hit the expected liability buckets. Confirm whether time tracking is bundled or billed separately so your true cost per hour stays accurate. Clean job costing evidence helps service and construction operators defend pricing.
OnPay is practical payroll software for hourly employers that want one flat plan covering overtime calculations, garnishment-friendly registers, and integrations with common time clocks or scheduling tools. Support picks up when a manager forgets to approve punches before cutoff. Use early payrolls to prove automated tax deposits, break rules configured for your state, and PTO balances if you track them inside payroll. Import a noisy week—split shifts, callbacks, and a holiday premium—to see if rounding or approval rules behave the way your policy states. Map GL exports once if QuickBooks or another ledger receives entries so location or department tags survive. Predictable pricing helps thin-margin operators schedule cash confidently.
Head-to-head comparisons to narrow your choice.
Gusto and QuickBooks Payroll both handle W-2 and 1099 payroll with automatic tax filing, but they target different workflows. Gusto is a sta…
Compare →Gusto and OnPay both serve small businesses with payroll, tax filing, and benefits, but they take different approaches. Gusto offers more HR…
Compare →QuickBooks Payroll and OnPay both serve small businesses with payroll and tax filing, but they take different approaches. QuickBooks Payroll…
Compare →For more options across all use cases, see our best payroll software roundup. To compare platforms side-by-side, see our payroll software comparisons.
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