Before you start

My Number
Ward registration
Employment records, fellowship documentation or business accounts
A determination of your residence status for tax purposes

Step-by-step

1
Understand the three tax residence categories
A non-resident is taxed only on Japanese-source income. A non-permanent resident — broadly, someone without Japanese domicile resident five years or less in the past decade — is taxed on Japanese income plus foreign income remitted to Japan. A permanent resident for tax purposes is taxed on worldwide income. The category changes automatically over time.
OnlineWho: You
2
Let the year-end adjustment handle it if you are a straightforward employee
Employers run nenmatsu chōsei in December, reconciling the year's withholding against what you actually owe. Most employees never file a return at all.
Via employerWho: YouDecember
3
Check the tax treaty if you are a researcher or teacher
Japan's tax treaties with many countries contain specific articles exempting visiting researchers, professors and teachers from Japanese income tax for a limited period, usually two years. This is genuinely valuable, it applies to a large share of Kyoto's incoming foreign population, and it requires an application filed through your institution before the first payment. Ask the university's administrative office directly.
Via employerWho: YouBefore your first salary payment
4
Budget for residence tax arriving in your second year
Jūminzei is assessed on the previous calendar year's income and billed from June. Your first year produces almost none because the assessment year had no Japanese income; your second year is the real number.
OnlineWho: You
5
Appoint a tax representative before leaving Japan
If you leave partway through a year you may still owe residence tax on income already earned. Appointing a tax representative before you go is the clean solution; leaving without doing so creates a debt that is difficult to settle from abroad.
In personWho: YouBefore departure
6
Know about Kyoto's accommodation tax if you ever let a room
Kyoto levies a lodging tax on paid accommodation, raised substantially from 2026 with a higher top band. It falls on guests and is collected by the operator — so it matters if you sublet, run a guesthouse, or host paying visitors, all of which are separately regulated here.
OnlineWho: You

Documents you’ll need

My Number
Gensen chōshūhyō — the annual withholding statement from your employer
Tax treaty application form, for eligible researchers and teachers
Records of any foreign income and overseas assets
Japanese bank details

Things most newcomers don’t know

The researcher and teacher tax treaty exemption is worth thousands and is routinely missed.

Many of Japan's bilateral tax treaties exempt visiting researchers, professors and teachers from Japanese income tax on their institutional salary for a defined period, commonly two years. Given how much of Kyoto's foreign population arrives through its universities and research institutes, a large number of people are eligible. It is not applied automatically — a form must go through the institution to the tax office before the first payment. Ask on your first day, not in your second year.

Source: National Tax Agency

Residence tax is billed a year in arrears, producing a second-year shock and an exit trap.

Jūminzei is calculated on the previous calendar year's income and collected from the following June. Arrive and your first year is nearly free of it; your second carries the full amount for your first year's earnings. If you leave Japan you can still owe residence tax on income already earned and spent. Settle it or appoint a tax representative before going.

Source: National Tax Agency

Non-permanent resident status shields foreign income, and it expires.

For roughly the first five years, a foreign national without Japanese domicile is taxed on Japanese-source income plus foreign income actually remitted into Japan — not on worldwide income. After that you become a permanent resident for tax purposes and Japan taxes everything. The switch is not announced and the consequences for anyone with overseas investments are significant.

Source: National Tax Agency

Furusato nōzei lets you redirect part of your residence tax and receive goods for it.

The hometown tax donation scheme allows residents to donate to a municipality of their choice, deduct almost all of it against residence and income tax, and receive a return gift worth a meaningful fraction of the donation. It is entirely legitimate, widely used by Japanese residents, and almost unknown among foreign ones.

Source: Ministry of Internal Affairs and Communications

Common mistakes to avoid

Missing the tax treaty exemption for researchers and teachers by not applying before the first salary payment.
Budgeting from your first year, when residence tax is almost nil.
Leaving Japan without settling residence tax or appointing a tax representative.
Not knowing when your non-permanent resident status expires and worldwide taxation begins.
Subletting or hosting paying guests without understanding Kyoto's lodging tax and accommodation rules.

Some of this may be out of date. Spotted something inaccurate? Help us keep it right for the next newcomer.