File the outstanding return, check the penalty notice and deal with unpaid tax promptly. The penalty rules depend on the tax year and whether the new MTD regime applies. No tax to pay does not automatically remove a late-filing penalty.
For dates and preparation before the deadline, use the preventive guide on Self Assessment deadlines. This page is for when you are already late, or about to be.
Which penalty regime applies?
Do not blend these two systems.
Classic Self Assessment penalties (the familiar £100 / daily / percentage-or-£300 structure) still apply to tax years that are not under the new Making Tax Digital for Income Tax penalty rules. That includes previous tax years after you join MTD. Example from GOV.UK: if you use MTD from 6 April 2026, the current (classic) penalties still apply to your 2025 to 2026 return deadline of 31 January 2027.
New MTD Income Tax penalties apply from the tax year you join Making Tax Digital for Income Tax. They replace the classic late submission and late payment penalties for your personal tax return for that year onward (with limited exceptions such as some trust, estate, partnership or non-resident company returns). See GOV.UK: Penalties for Making Tax Digital for Income Tax.
If you are unsure which year and regime you are dealing with, check your HMRC messages and the two GOV.UK pages linked in the sources. Do not assume the amounts below apply to every return forever.
Classic Self Assessment late filing penalties
Where the classic regime applies, GOV.UK sets out that if you need to send a Self Assessment tax return and you send it late, you can get:
- an initial £100 penalty
- after 3 months, daily penalties of £10 per day, up to a maximum of £900
- after 6 months, a further penalty of 5% of the tax due or £300, whichever is greater
- after 12 months, another 5% or £300 charge, whichever is greater
Partnership returns can create penalties for each partner when the partnership return is late. GOV.UK also notes a separate “failure to notify” risk if you register late after 5 October and do not pay your bill by 31 January. Check the Self Assessment penalties page for the wording that applies to you.
Classic late payment penalties
Under the classic rules, paying late can bring penalties of 5% of the unpaid tax at 30 days, 6 months and 12 months, plus interest. Filing on time but leaving the bill unpaid is still a problem.
MTD-era late submission and late payment
Once the new MTD penalties apply for a tax year, late submission uses penalty points rather than the classic £100 starting charge for that year’s return (and, after 2026 to 2027, for quarterly updates too).
In outline for people required to use MTD: the point threshold is 4; reaching it brings a £200 penalty, with further £200 charges for later missed deadlines while at the threshold. For 2026 to 2027 specifically, HMRC will not apply penalty points for late quarterly updates. Points can still apply for a late tax return for that year, and you still need to send quarterly updates before you can submit the return.
Late payment penalties under MTD are also different. They are proportionate to how long the tax stays unpaid (with a longer “first year” window), and they do not apply to payments on account. Late payment interest still applies. Full tables and conditions are on the GOV.UK MTD penalties page. This summary is not a substitute for that page.
What to do now
- File the outstanding return with the best complete information you can support.
- Pay what you can and use HMRC’s published payment routes if you need time.
- Read any penalty notice. Payment deadlines and appeal rights matter.
- Consider a reasonable excuse appeal only where it genuinely fits. “I was busy” is rarely enough on its own.
- Prevent a repeat with earlier document gathering, or accountant help for the next cycle.
If you need a return prepared properly rather than guessing alone, TaxSimba’s Self Assessment service works from documents you provide. An accountant prepares and reviews, and you approve before filing where that step applies. We do not guarantee penalty cancellation. Related reading: documents checklist, payments on account, and how to amend a return if the figures themselves need correcting after you file.
Match each charge to the notice
Illustrative preparation example.
You receive a late-filing penalty and a separate late-payment charge. Record the year, type, amount and issue date for each. Filing the return deals with the missing submission, while payment and any appeal need separate action.
Check: Have you checked the applicable regime and response deadline for each individual notice?
| Check | Practical action |
|---|---|
| Which return and tax year are overdue? | Identify the year and applicable penalty regime before using a penalty calculator. |
| Is filing, payment or both outstanding? | Progress the return and the payment discussion separately; an inability to pay does not remove filing duties. |
| Does the notice offer an appeal route? | Record its deadline and prepare a factual timeline with supporting evidence. |
Will joining MTD cancel an older penalty?
No. Earlier tax years keep the rules that apply to them. Read the notice for the particular obligation rather than assuming new software resets the account.
Can I wait for an appeal decision before filing?
An appeal does not itself remove an outstanding return. Complete the required filing and follow the notice's instructions on payment while the appeal is considered.
Download a checklist for this guide
- Identify every outstanding tax year.
- Copy the notice date, charge and appeal deadline.
- List missing filing records and who will supply them.
- Prepare a dated explanation with supporting evidence.
- Record filing confirmation and any payment arrangement separately.