Two systems, one goal: getting your tax right
If you earn a salary in Japan, you have almost certainly heard the term 年末調整 (nenmatsu chosei, "year-end adjustment") without ever really doing anything for it. Some residents, meanwhile, spend every February and March filling out a 確定申告 (kakutei shinkoku, "final tax return"). Both exist to do the same basic job — make sure the income tax you paid over the year matches the tax you actually owe — but they work in very different ways and apply to different people. Understanding which one applies to you (sometimes both) is the first step to avoiding a missed refund or an unfiled return. For a broader starting point, see our guide on whether you need to file taxes in Japan at all.
年末調整: the employer-run reset button
For most salaried employees with a single employer, 年末調整 is the entire tax process. Each month your employer withholds an estimated amount of income tax from your paycheck. In December, your employer recalculates your actual tax liability for the year — factoring in your final income and eligible deductions — and adjusts your last paycheck of the year to square the difference. According to the National Tax Agency (NTA No.1900), most single-employer salaried workers are fully settled through this process and never need to touch a tax return.
Your employer can apply several common deductions directly within 年末調整, including:
- 生命保険料控除 (life insurance premium deduction)
- 社会保険料控除 (social insurance premium deduction)
- 住宅ローン控除 (housing loan tax credit) — but only from the second year onward
If your situation is simple — one employer, no major side income, no medical bills to speak of — 年末調整 alone likely settles your taxes for the year.
確定申告: when you file it yourself
確定申告 is the self-filed return that covers everything 年末調整 does not. It has its own annual filing season, typically running from mid-February to mid-March, during which you report your income and deductions directly to the tax office. This is the mechanism used by freelancers, business owners, and anyone whose tax situation is more complex than a single, simple salary.
Comparison at a glance
| Aspect | 年末調整 (Year-End Adjustment) | 確定申告 (Final Tax Return) |
|---|---|---|
| Who does it | Your employer | You, yourself |
| When | December, through your final paycheck | Filing season, mid-February to mid-March |
| What it covers | Salary income plus a limited set of deductions | All income types and all deductions, including ones the employer cannot process |
| Typical filer | Single-employer salaried worker with a simple tax situation | Freelancers, multiple-employer earners, high earners, anyone with unprocessed deductions |
When 年末調整 isn't enough
You'll need to file 確定申告 yourself in several common situations:
- Your salary exceeds ¥20,000,000 — above this threshold, no 年末調整 is performed at all
- You have more than ¥200,000 in income outside your salary (see our explainer on the 20万円 rule)
- You worked for two or more employers during the year
- You have freelance or business income — start with our guide for freelancers filing their first year in Japan
- You want to claim a deduction your employer cannot process through 年末調整
That last point matters more than people expect. Some deductions simply fall outside what an employer's year-end paperwork can handle, even if you're an ordinary salaried employee. These include:
- 医療費控除 (medical expense deduction)
- ふるさと納税 contributions beyond the one-stop exception system
- 住宅ローン控除, but only in its first year of use — from year two, your employer can take over
If any of these apply to you, you'll file 確定申告 even if your income itself is straightforward salary income.
A quick way to think about it: 年末調整 handles the routine case. 確定申告 handles everything routine doesn't cover — extra income, extra deductions, or income above the threshold where year-end adjustment stops applying entirely.
Left a job mid-year? You may be owed money
If you left a job partway through the year and were not included in that employer's 年末調整, there's a good chance too much tax was withheld from your paychecks relative to what you actually owed. In this case, the NTA notes (NTA No.1910) that filing a 還付申告 (refund return, kanpu shinkoku) is usually the way to get that overpayment back. A 還付申告 is really just a friendly subtype of 確定申告 — same form, same process, except you're claiming a refund rather than paying additional tax. The good news is you don't need to rush: you generally have up to five years to file and claim it.
Not sure which one applies to you?
Every situation is a little different, and the categories above can overlap — for instance, you might be fully covered by 年末調整 for your salary but still need to file 確定申告 separately for a medical expense deduction or a bit of side income. When in doubt, working through your specific numbers against the thresholds above is the most reliable approach. Our FAQ page covers many of the edge cases readers ask about most often.
This article is general information based on published NTA guidance and is not tax advice. Individual circumstances vary, and for anything beyond a routine situation it is worth confirming details with the NTA or a licensed tax professional.
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