Guide · US retirement, Medicare, overtime and time

How to Reconcile Timesheet Hours With Payroll Records

By Abdul Baseer · Published · Updated · 5 min read

In short

To reconcile timesheet hours with payroll records, export approved hours and payroll hours for the same dates, make the employee IDs match, and compare the total per employee. Review missing employees first, then duplicate rows, then differences, largest first, and correct the source data before payroll closes.

Why do timesheet and payroll hours differ?

Most differences are data differences, not pay errors: different pay-period dates, ID formats, rounding, unpaid breaks, hours approved after the export, manual adjustments and duplicate rows. A few are real pay errors, which is why the check is worth doing before payroll closes.

Prepare the two files

Export approved hours and the payroll hours for the same dates. One header row, one entry per row, no subtotal rows. Save as CSV or copy the cells.

How do you match employee IDs and pay periods?

Make the ID format the same (leading zeros are the usual culprit) and confirm both files cover the same first and last day. If a workweek is split across two pay periods, compare complete workweeks or use the workweek-boundary checker for the overtime.

Check missing, duplicate, and mismatched rows

Use the tool above. Review in this order: employees missing from one file, then exact duplicate rows, then employees whose totals differ, largest difference first.

Review breaks, rounding, and overtime separately

Do not mix causes. A 30-minute gap may be an unpaid break; a 5-minute gap may be rounding; a gap of a full shift is a missing or extra day. Overtime is figured by workweek (not pay period), so check it separately.

Worked example

The tool’s sample files give 1 matching, 3 different, 1 only in the timesheet and 1 only in payroll. The net difference is -7.00 hours, but the absolute differences add to 23.00: a net figure can hide errors that cancel out, so always review line by line.

Pre-Payroll reconciliation checklist

  1. Same pay-period dates in both files.
  2. IDs formatted the same.
  3. No subtotal rows.
  4. Every employee in one file is in the other, or explained.
  5. Duplicate rows reviewed.
  6. Differences above your tolerance explained or corrected.
  7. Breaks, rounding and overtime reviewed on their own.
  8. Reviewer and date recorded; corrected data re-exported.

What should you do with the differences you find?

Treat each difference as a question, not a verdict. Start with the largest and with any employee who appears in only one file, because those are the likeliest to be a missing or extra day. For each one, go back to the source record, a time clock, a schedule or an approval, and decide whether the timesheet or the payroll export is the one that is wrong.

Correct the data in the system it came from, not in the export. Then export both files again and run the comparison until the review list holds only differences you can explain. Write down who reviewed it and on what date, so the check can be shown later.

How long should timesheets and payroll records be kept?

Under the federal wage-and-hour rules, payroll records must be kept at least three years and time cards at least two (29 CFR 516.5 and 516.6). Some states require longer, so check yours. Keep the comparison report with the pay-period records, because it shows what was checked and corrected before the payroll was paid.

Timecard CSV reconciliation toolPaste both files, press Load sample to see how it works, and download the review list as CSV.

Common questions

How do I compare timesheet hours with payroll hours?

Export both as CSV (or copy the cells from Excel), pick the employee and hours columns in each file, and compare the total per employee for the pay period. Anything that does not match, or appears in only one file, goes on a review list. The tool above does the matching and lists the differences with the rows to look at.

How do I find differences between two CSV files?

A general file-compare shows changed lines but does not know that "0012" and "12" are the same employee or that eight daily rows add up to one weekly total. For payroll, compare the totals per employee (or per employee per day), not the raw lines. That is what this tool does.

How do I reconcile employee hours before payroll?

1) Fix the pay-period dates in both files. 2) Make sure every employee ID uses the same format. 3) Compare hours per employee. 4) Review exceptions: missing people, duplicate rows, differences. 5) Check rounding, breaks and approvals separately. 6) Only then process payroll. The guide linked below has a printable checklist.

What should I check when timesheet hours do not match payroll?

In this order: the pay-period date range, the employee ID or name format, duplicate or missing rows, unpaid break deductions, the rounding rule, hours approved after the export, manual payroll adjustments, and which workweek the hours fall into. Most gaps are one of these.

Can I compare two Excel or CSV timesheets online?

Yes. Save the sheet as CSV, or select the cells in Excel, copy, and paste them into the box: copied cells arrive tab-separated and are read correctly. The tool does not open .xlsx files directly, and comma, tab, semicolon and pipe separators are detected automatically.

How do I find missing employees or duplicate rows in a payroll export?

Missing employees show as "Only in A" or "Only in B". Rows that are completely identical to an earlier row are listed as duplicate rows with their row numbers, and they are counted in the totals so you can see their effect. Check whether they are real before deleting anything.

Is it safe to upload payroll CSV data to an online tool?

With this tool nothing is uploaded: the file is read and compared in your browser and the code makes no network request with your data (you can confirm in the Network tab of your browser's developer tools). That is a statement about this tool only. Many other online tools do send files to a server, so check each one's privacy policy before you use real payroll data. Never paste Social Security numbers or bank details into any comparison tool; employee IDs and hours are enough.

Sources

Reviewed on 25 Oct 2026 against the published sources below. Laws and prices change, so check the current position before you rely on a figure.

Try the calculator

Timecard CSV reconciliation toolDuplicate timecard entry checker

Keep reading

How to find duplicate timesheet entriesHow to read a pay stub

This guide is general information, not legal, financial or religious advice. Figures are estimates worked out from the sources above and may differ from what applies to you. See the disclaimer. Found a mistake? Tell us.