Japan taxes you twice on the same income: national income tax (所得税), withheld from each payslip, and residence tax (住民税), paid to the city you lived in. The second one is where people get caught, because it arrives about a year after the money did.
Why the bill is late
Residence tax is assessed on your income for the previous calendar year, and billed from June through to May of the following year. If you arrived in Japan partway through a year, you had no Japanese income in the year being assessed, so you pay little or nothing at first.
The consequence is the part nobody warns you about: your second year in Japan costs more than your first, on identical pay. People budget on their first-year take-home and then find a new deduction appearing in June.
The year-end adjustment
For most employees, income tax is settled by the year-end adjustment (年末調整) in November and December. Your employer reconciles what was withheld across the year against what you actually owed, and the difference appears in a December or January payslip.
You are asked for declarations and certificates around November — dependants, life and earthquake insurance premiums, and any national pension or health insurance you paid yourself. Certificates you do not hand in are deductions you do not get, and they arrive by post in October and November, which is exactly when they look like junk mail.
When you have to file yourself
The year-end adjustment does not cover everyone. You generally need to file your own return (確定申告) between 16 February and 15 March for the previous year if any of these apply:
- Your employment income was above ¥20 million
- You had a second employer, or side income above ¥200,000
- You left a job partway through the year and were not adjusted by a new one
- You are claiming the medical expenses deduction, or a housing loan deduction for the first year
- You used furusato nozei with more than five municipalities, or without the one-stop exception
What changed in the 2025 reform
The basic deduction (基礎控除) rose from ¥480,000 to ¥580,000 for most taxpayers, applying from the 2025 tax year and reflected in the year-end adjustment from December 2025. A further temporary uplift raises the point at which income tax starts to around ¥1.6 million for lower incomes, replacing the old ¥1.03 million threshold that part-time earners used to work around.
Two cautions. The bands are tiered, so the figure that applies to you depends on your total income — and residence tax thresholds are set separately from income tax ones, so crossing one does not mean crossing the other. Confirm your own position with the National Tax Agency or your employer rather than a summary.
Furusato nozei, briefly
Donations under furusato nozei (ふるさと納税) must be made by 31 December to count against that year. It moves tax you already owe to another municipality in exchange for goods, so it is one of the few items here that is worth money rather than costing it. Your deductible ceiling depends on your income and household — overshoot it and the excess is simply a donation.
Where to confirm this
- National Tax Agency — income tax, filing dates, deductions
- Your city or ward office — residence tax, payment slips, and appointing a tax representative
Guides are dated rather than undated: last reviewed 6 August 2026. This is an organisational aid, not legal or immigration advice — always confirm anything consequential with your ward office, the Immigration Services Agency, or a qualified professional.