Tax

For tax, Japan classifies you as non-resident, non-permanent resident, or permanent resident — separate from your immigration status. Broadly: non-residents are taxed only on Japan-source income; non-permanent residents (in Japan under 5 of the last 10 years, without permanent intent) are taxed on Japan-source income plus foreign income paid in or remitted to Japan; permanent residents (for tax) are taxed on worldwide income. This affects foreign income and investments, so confirm your category with the NTA or a tax accountant.

Many employees do not, because tax is settled by year-end adjustment (年末調整). You generally must file (確定申告) if you have side income over ¥200,000, two or more employers, self-employment income, sizeable investment or crypto gains, or you want to claim deductions like large medical costs or a first-year mortgage credit. Filing season is Feb 16 – Mar 15 via e-Tax. When unsure, check the NTA guidance or ask a 税理士.

Resident tax (住民税, about 10%) is charged the year after the income is earned, based on the previous year’s income. So in your first year you often pay little, and in your second year you get a bill for your full first-year income. The same lag means people who stop working or leave Japan can still owe resident tax afterward. Budget for it in advance.

Furusato Nozei (ふるさと納税) lets you donate to local governments and receive local gifts (food, goods) while deducting almost all of the donation from your resident and income tax — you effectively pay ¥2,000 out of pocket for the gifts. It is worth it for most taxpayers with sufficient income, up to a limit based on your income and family situation. Use the official rules and a limit simulator, and keep the paperwork (One-Stop or tax return) to claim the deduction.

Crypto profits are treated as miscellaneous income (雑所得) and taxed at your marginal rate — combined with resident tax this can reach roughly 55%, unlike the ~20% flat rate for listed stocks. Every disposal is taxable, including selling for yen, trading one crypto for another, and spending crypto on goods. You must track cost basis and calculate gains, so recordkeeping tools are important, and larger activity often warrants a tax accountant.

It is income after related expenses, not gross revenue. A one-job employee generally must file a national return when non-employment, non-retirement income exceeds ¥200,000 (measured after expenses). Exactly ¥200,000 does not trigger it — the rule is “exceeds.” Importantly, even below ¥200,000 your municipality usually still expects a resident-tax declaration of that income, so the ¥200,000 relief is national-tax only.

An income deduction (所得控除) reduces the income you are taxed on, so its value is roughly your marginal rate times the deduction — a ¥300,000 medical deduction at a 20% rate saves about ¥60,000 of national tax, plus some resident tax. A tax credit (税額控除), such as the housing-loan credit, reduces the calculated tax directly, so a ¥300,000 credit can cut tax by up to ¥300,000. A deduction is not a refund of its full amount.

Deduct qualifying medical costs you paid in the year for yourself or family sharing your livelihood, minus reimbursements and a ¥100,000 threshold (or 5% of total income if that is below ¥2M), capped at a ¥2M deduction. Example: ¥500,000 costs − ¥100,000 reimbursement − ¥100,000 threshold = ¥300,000. You file a return (not year-end adjustment), submit a statement, and keep receipts five years. You cannot combine it with the self-medication deduction in the same year.

No. Year-end adjustment (年末調整) is your employer reconciling the income tax on the salary they paid, applying the basic, spouse, dependent, social-insurance, and insurance deductions. A final return (確定申告) is you reporting all income. Even after year-end adjustment you must file for side income over ¥200,000, medical expenses, donations beyond one-stop, or the first mortgage-credit year. Year-end adjustment does not cure unreported side, rental, overseas, or investment income.

You can still file late (期限後申告), and filing voluntarily before the tax office contacts you reduces the non-filing penalty. Separately, delinquent tax (延滞税) accrues on unpaid tax from the day after the deadline — roughly 2.8% then 9.1% in 2026. Concealment triggers a heavier aggravated penalty. If you cannot pay, contact the tax office about a grace of payment (up to a year) rather than ignoring the bill.

No — it is taxable sales in the base period (for an individual, normally the year two years earlier), not profit. A low-margin business with high turnover can be liable while a high-profit consultancy with modest billings may not. The exemption can also be lost by the specified-period test, a voluntary election, succession, or — importantly — registering as a qualified-invoice issuer, which makes you taxable regardless of sales.

It depends on your clients. Registering as a qualified-invoice issuer lets business customers claim input-tax credit on what they pay you, but it makes you liable for consumption tax you were exempt from. Weigh how much revenue comes from business clients who need input credit, and the risk of lost work or discounts, against the tax and compliance cost. The temporary 20% special measure can cap early-year liability. This is a good first-registration question for a 税理士.

Yes, if you file. A listed-share loss can be offset against listed-share gains and, by election, eligible dividends, and any remaining loss carries forward up to three years — but only if you file a return every year in the window, even a no-gain year. Note NISA losses cannot offset taxable gains, and filing to use losses also adds the income to resident-tax measures, which can raise health-insurance premiums.

Generally yes. The US taxes citizens and green-card holders on worldwide income even while resident in Japan, so you usually file in both countries. The foreign tax credit and foreign earned income exclusion reduce double taxation but must be claimed on a US return. Japanese accounts and funds can trigger FBAR, FATCA, and possible PFIC issues that Japanese tax software does not handle — use a Japan 税理士 together with a US CPA/EA.

Complete the departure-year return before leaving, or appoint a tax agent (納税管理人) to file afterward from within Japan. Resident tax on the prior year survives departure, so arrange payment with your municipality. Test exit-tax exposure (it can apply at ¥100M of specified financial assets), and if you had employee pension, consider a lump-sum withdrawal — a tax agent can often reclaim much of the 20.42% withheld by applying retirement-income treatment.