A calculator works out a whole tax year and divides it; payroll works out one pay period at a time using the thresholds prescribed for that period. Even when both are right they can differ by pennies. When they differ by more, the cause is almost always a mid-year start, a non-cumulative tax code, an unusual month, or a pension or benefit the calculator was not told about.
They are two different sums
A whole-year calculation asks what a full tax year on this salary produces, then spreads the answer. Payroll never does that. Each pay day it applies the free pay, the band limits and the National Insurance thresholds that are prescribed for that one period.
Those period figures are published in their own right rather than derived by division. On a monthly payroll for 2026/27, National Insurance starts at £1,048 for the month; on a weekly one it starts at £242. The monthly threshold is not the weekly one times four and a third, and the annual one is not twelve times the month.
On £35,000 a year with code 1257L, the annual view comes to £2,393.34 a month. A payslip can sit a few pence either side of that with nothing wrong at all.
You started part-way through the tax year
A calculator assumes twelve months on this salary. If you started in July, you have four months of unused Personal Allowance behind you, and a cumulative tax code gives it back to you over the rest of the year. Your first payslips will show less tax than a twelfth of the annual figure, sometimes none at all.
The same works in reverse if you have already been paid this tax year by another employer. Your P45 carries those figures across, and your new employer's cumulative calculation takes them into account, so the tax on your first payslip reflects the year so far rather than the new job on its own.
Your code is being operated on week 1 or month 1
A code ending in W1, M1 or X taxes each pay period on its own. Your employer gives one period of allowance and cannot hand back tax overpaid earlier in the year.
On a monthly payroll, one period of the standard code is £1,048.26 of tax-free pay. That is the right amount for one month and the wrong amount for someone who has months of unused allowance behind them, which is why an emergency code and a calculator disagree most for people who started late in the year.
The month was not a typical one
Overtime, a bonus, commission, a backdated pay rise or unpaid leave all land in a single pay period. Income tax on a cumulative code mostly evens out across the year, but National Insurance does not: it is charged period by period, so a spike is charged at the main rate up to the period's upper limit and at the lower rate above it, and a quiet month gets nothing back.
A student loan deduction behaves the same way. It is worked out on the pay in that period, so one large month can produce a repayment even for someone whose annual salary is below the annual threshold.
You are not paid monthly
A four-weekly payroll makes thirteen payments in a year, not twelve, so every payment is smaller than a month's pay and the annual total is the same. On £35,000 a year, a four-weekly cycle takes home £2,209.24 each time against £2,393.34 a month.
Four-weekly and fortnightly payrolls also use their own National Insurance thresholds. The four-weekly primary threshold for 2026/27 is £967, which is not four times the weekly figure: the regulations divide the annual amount and round up once at the end, and the two routes give different answers.
A weekly payroll adds one more wrinkle. Some tax years contain fifty-three weekly pay days rather than fifty-two, and the extra one is handled by a special rule that can leave a small underpayment to settle after the year end.
Your pension works differently from the one assumed
The three methods produce three different payslips for the same contribution. Salary sacrifice reduces your gross pay before anything is worked out, so both income tax and National Insurance fall. A net pay arrangement takes the contribution before income tax but after National Insurance. Relief at source takes it after both, and the scheme reclaims basic-rate relief into the pot rather than into your pay.
Choosing the wrong one in a calculator moves the take-home figure by more than most people expect, and it is the single most common reason a pensioned payslip does not match.
Your tax code is not the standard one
Company benefits, untaxed income, a Marriage Allowance transfer or tax owed from an earlier year all change the number in your code, and a calculator run on the standard code will not know. The code on your payslip is the instruction your employer is following, so it is the figure to type in.
A student loan threshold is worth checking at the same time. The borrower-facing page on GOV.UK rounds the period thresholds to whole pounds for readability, but payroll uses the published figure to the penny: on Plan 2 that is £2,448.75 a month against an annual threshold of £29,385. A pound of threshold is enough to change the deduction for anyone paid close to the line.
The gross figure itself is different
Shift premiums, a car allowance, an on-call payment, a salary sacrifice for a car or a cycle, statutory maternity or sick pay, and any month with unpaid absence all change the gross figure before a single deduction is worked out. A calculator told an annual salary cannot see any of them.
Start from the gross pay printed on the payslip rather than from your contract, and most of the remaining difference disappears.
How to find which one it is
Work in this order. Compare the gross figures first, then the tax code, then the pay period, then the year-to-date columns. A mismatch in the first three explains almost every case, and the year-to-date columns settle the rest by showing what the cumulative calculation is actually working from.
If the gross, the code and the period all agree and the deductions still do not, that is worth reporting. Our method, and the sources behind every figure, are published so a disagreement can be checked rather than argued about.