CSLM11114 - FAQs: borrowers questions and answers: my employer has deducted too much
As deductions are calculated on a non cumulative basis, your employer may still have deducted repayments in certain periods, even if your earnings for the year are less than the annual threshold. For example, if you were paid a bonus or overtime that put you over the threshold for your plan and or loan type in that period.
Once your loan is paid in full, HMRC will instruct your employer to stop making dedcutions via a Stop Notice. However, this can take around 4 weeks for the employer to action which means you may pay back more than you owe. If this is the case you can request a refund.
For more information on how to ask for refund if you repaid more than you should, access the gov.uk website.