Paycheck difference diagnosis
Find the first line that differs from your actual paycheck
Reconcile gross pay first, then taxable wages, each tax and finally cash deductions. The first disagreement usually tells you which input or unsupported payroll rule to investigate. A different net result alone does not prove an employer made a mistake.
This checklist is for ordinary US wages using 2026 rules. PaycheckIndex estimates a regular payment, not every payroll provider's method, nonresident adjustment, bonus method or special benefit arrangement.
Start with the same payment, not just the same salary
A $78,000 annual salary is $3,000 over 26 checks and $3,250 over 24 checks. Biweekly and twice-monthly are different frequencies. A partial first check, unpaid leave, overtime or a bonus also breaks the assumption that every check equals annual salary divided by a fixed frequency. Use the actual current gross when reconciling; do not treat a one-time payment as a recurring annual raise.
| First mismatch | Evidence to collect | Next check |
|---|---|---|
| Gross pay | Hours, rates, pay dates and current earnings | 26 vs 24 checks; partial period; bonus or overtime |
| Federal taxable wages | Benefit elections and taxability per deduction | Traditional retirement vs Roth; premium entered twice |
| Federal withholding only | Effective W-4 and payroll method | Steps 2-4; old W-4; supplemental payment |
| Social Security / Medicare | Each tax's YTD wages before this check | Wage cap crossing; Additional Medicare; FICA exclusions |
| Deposit only | After-tax deductions and bank allocations | Roth, loan, garnishment, split deposit or reimbursement |
A $99.20 difference caused by missing year-to-date wages
Assume a regular $3,000 payment has no FICA-exempt deductions. Social Security wages before this check are $183,100 and Medicare wages before this check are also $183,100. Only $1,400 remains under the 2026 Social Security cap. Correct current Social Security is $1,400 x 6.2% = $86.80.
Leaving the YTD input at zero produces $186.00 instead. That overstates Social Security by $99.20 and understates estimated take-home pay by the same amount. Regular Medicare remains $43.50; no Additional Medicare starts in this example. Current federal withholding is unchanged by the Social Security cap.
Reproduce the wage-cap crossing. With the illustrated single W-4, federal withholding is $320.38 and net pay is $2,549.32. The $78,000 annualized input describes this current recurring payment, not total earnings already received: earlier bonuses or a pay change can make YTD wages much higher.
Use the correct employer and wage history
Ordinarily, an unrelated new employer tracks its own Social Security wages. Importing every former employer's wages into this input can stop withholding too early. The separate two-employer Social Security guide explains the return-level reconciliation. Medicare and Social Security YTD wages can differ, so do not copy a single gross-pay total into both fields without checking.
Recognize an amount the model does not cover
For income-tax states, this calculator needs the state/local withholding amount; selecting the state does not calculate its income tax. Alaska and Washington have separately modeled employee contributions. An exemption or different covered-wage definition can change those contributions. Roth contributions, garnishments and other after-tax cash deductions must be reconciled outside the current tool.
For a bonus, check the employer's supplemental-wage method before comparing it to a regular salary estimate. A 2019-or-earlier W-4, a permitted wage-bracket or alternative method, and nonresident treatment can also require a calculation this tool does not reproduce.
Common rounding and privacy mistakes
A few cents can arise from rounding individual lines versus a final total. Publication 15-T also permits specified whole-dollar rounding, so not every small difference is a coding error. Resolve wage bases and settings before changing rounding. When asking payroll about a larger difference, identify the pay date, disputed line, expected calculation and W-4 effective date. Keep the SSN and bank account number out of any public screenshot or shared calculator URL.
Sources checked September 7, 2026: 2026 Publication 15, 2026 Publication 15-T, methods and rounding, SSA wage base, and IRS Topic 608, excess Social Security withholding. The difference example was constructed to isolate one input.