Paying Self Assessment, penalties and refunds
Filing late and paying late are two separate failures with two separate sets of penalties, and they run at the same time. On a £5,000.00 bill left a year, they add up to £2,350.00 before interest.
Updated 11 September 2026 · Return for the tax year ended 5 April 2026
How to pay Self Assessment #
The deadline is 31 January 2027, and what counts is the day the money reaches HMRC, not the day you send it. If the deadline falls on a weekend, it has to be there the working day before.
| How you pay | Time to reach HMRC |
|---|---|
| Approving a payment through your online bank | Same or next day |
| Online or telephone banking by Faster Payments | Same or next day |
| CHAPS | Same or next day |
| Debit card or corporate credit card online | Same or next day |
| Direct Debit already set up | Around 3 working days |
| Direct Debit set up for the first time | Around 5 working days |
You cannot pay by personal credit card. If a payment is going to be late anyway, paying part of it still helps, because the percentage penalties are charged on what is unpaid at each milestone rather than on the original bill.
Self Assessment penalties for filing late #
These apply whether or not you owe anything. A nil return filed late still collects the first penalty, which is why people who think they have nothing to declare should file rather than assume it does not matter.
| How late | Penalty | Note |
|---|---|---|
| The day after the deadline | £100 | Charged even if you owe no tax at all |
| 3 months late | £10 a day, up to £900 | Daily penalties run for a maximum of 90 days |
| 6 months late | 5% of the tax due, or £300 | Whichever is greater, on top of the above |
| 12 months late | Another 5%, or £300 | Whichever is greater, again on top |
Self assessment late payment penalties #
A completely separate set, charged on the tax still outstanding at each point, plus interest running from the day after the due date.
| How late | Penalty |
|---|---|
| 30 days late | 5% of the tax unpaid |
| 6 months late | A further 5% |
| 12 months late | A further 5% |
What being late actually costs #
Take a £5,000.00 tax bill, neither filed nor paid, and follow it forward.
| How late | Filing penalties | Payment penalties | Total on top of the tax |
|---|---|---|---|
| 1 month | £100.00 | £250.00 | £350.00 |
| 6 months | £1,300.00 | £500.00 | £1,800.00 |
| 12 months | £1,600.00 | £750.00 | £2,350.00 |
£2,350.00 on a £5,000.00 bill is 47% added, before interest. And note how much of it is the filing side: £1,600.00 of the £2,350.00 would have been avoided entirely by sending the return in on time, even with the money still unpaid.
Self Assessment repayments and refunds #
A Self Assessment repayment happens when you have paid more tax during the year than the return says you owed. It is common for anyone taxed at source on a flat rate, which is why it is the normal outcome for CIS subcontractors: 20% comes off every payment without any regard for the Personal Allowance or expenses.
Nothing arrives automatically. The repayment is only triggered once the return is filed and processed, so an overpayment simply sits with HMRC until you act. Once approved it usually reaches a bank account within a few working days, though HMRC may hold it for security checks, and it can be set against other tax you owe instead of being paid out.
If you work under CIS, the CIS refund calculator estimates what you are likely to be owed before you file, and claiming your CIS refund covers the process.
Self assessment late filing penalties, and a repayment that has not arrived #
Self assessment late filing penalties are the fixed ones in the table above, and they apply whether or not tax is owed. The late payment penalties are separate and run alongside them.
In the other direction: a self assessment bank repayment pending status means HMRC has approved your refund and it is queued for payment rather than stuck. It usually clears within a few working days, and can sit longer if HMRC is running security checks, which happens more often on a first repayment or where bank details have recently changed.
Self assessment tax payment online is the fastest route either way, and the payment reference is your UTR followed by the letter K.
Spreading the bill #
There are two different things here and they are constantly confused. One is for people who can pay but would rather not pay it all at once. The other is for people who cannot pay.
A Budget Payment Plan is the voluntary one. You set up a Direct Debit and put money aside towards a bill that is not due yet, weekly or monthly, at whatever amount you choose. It is available only if you are up to date with everything, and you can stop it whenever you like. It does not reduce the bill, it just stops January arriving all at once.
Time to Pay is the other one, for a bill you already owe and cannot settle. It is an arrangement with HMRC to pay in instalments, and smaller debts can often be set up online without speaking to anyone. Interest still runs for the whole period, but the late payment penalties can be avoided if the arrangement is agreed early enough.
Either way the return still has to be filed on time. Neither arrangement does anything about the filing penalties, which as the table above shows are the larger half of the cost.
Appealing a penalty #
You can appeal if you have a reasonable excuse, normally within 30 days of the penalty notice. HMRC accepts things genuinely outside your control: serious illness, a bereavement close to the deadline, a fire or flood, a failure of HMRC's own service, or postal delays beyond your control.
It does not accept not having the money, finding the return difficult, relying on someone else who let you down, or not knowing about the deadline. If the excuse ends, the return has to go in as soon as reasonably possible afterwards, or the appeal fails anyway.
Common questions #
How do I pay my Self Assessment bill?
Through your HMRC online account by approving a payment from your bank, by debit card, by Faster Payments or CHAPS, or by Direct Debit. Faster payment methods reach HMRC the same or next working day. A first-time Direct Debit needs several working days, so it is not a last-minute option.
What reference do I use to pay Self Assessment?
Your UTR followed by the letter K. Ten digits and a K, with no spaces. Using the UTR on its own, or a company reference, is the most common reason a payment is not matched to the right account.
What is the penalty for filing a Self Assessment return late?
£100 the day after the deadline, even if you owe no tax. After 3 months, £10 a day up to £900. After 6 months, 5% of the tax due or £300, whichever is greater. After 12 months, the same again.
What is the penalty for paying late?
5% of the tax still unpaid at 30 days, another 5% at 6 months, and another 5% at 12 months, plus interest running from the day after the due date. These are separate from the filing penalties and can apply at the same time.
What does a year of being late actually cost?
On a £5,000 bill, twelve months late and unpaid, the filing penalties come to £1,600 and the late payment penalties to £750. That is £2,350 on top of the tax, before interest.
How long does a Self Assessment refund take?
Once a repayment is approved it usually reaches a bank account within a few working days, though HMRC may hold it for security checks. A repayment is only triggered once the return is filed and processed, so an overpayment sits with HMRC until you file.
Can I appeal a Self Assessment penalty?
Yes, if you have a reasonable excuse, normally within 30 days of the penalty notice. Serious illness, a bereavement, a fire or flood, or an HMRC service failure can qualify. Not having the money, or finding the return difficult, does not.