Before you start

A residence card (zairyū card) and a registered address at your ward office
A My Number (Individual Number), issued after you register your address
Employment with a company that runs payroll withholding (nearly all do)
Your bank account and, for the year-end adjustment, certificates for any deductions you want to claim

Step-by-step

1
Tax is withheld automatically from each paycheck (gensen chōshū)
Your employer deducts national income tax (5%-45% progressive, plus a 2.1% reconstruction surtax) from every salary payment and remits it on your behalf. You do nothing — this is why most employees never deal with the National Tax Agency directly.
Via employerWho: Employer (payroll); automatic for the employeeEvery payday, year-roundNational income tax 5%-45% of taxable income + 2.1% surtax (withheld, not an extra fee)
2
Complete the year-end adjustment (nenmatsu chōsei)
Around November-December your employer hands you 1-2 declaration forms (dependents, insurance, basic deduction). Fill them in and attach certificates for deductible items — life/earthquake insurance, your own pension/health top-ups, and a spouse/dependents. Your employer recalculates your exact annual tax and refunds any over-withholding (or deducts a shortfall), usually in your December or January pay. This replaces filing a return for most people.
Via employerWho: Employee submits forms; employer reconcilesForms due by early-mid December; reconciliation in Dec/Jan payrollFree; often results in a refund
3
Receive your withholding statement (gensen chōshū-hyō)
After the year-end adjustment your employer issues a gensen chōshū-hyō — the one-page record of your annual income and tax withheld. Keep it: you need it to file a return, apply for a loan or visa renewal, claim a pension lump-sum on departure, or prove income.
Via employerWho: Employer issues to employeeIssued around January (or on departure if you leave mid-year)Free
4
File a final return (kakutei shinkoku) only if an exception applies
You must file your own return for the prior calendar year if you had side income over ¥200,000, two or more employers, salary over ¥20 million, you are leaving Japan mid-year, or you want deductions the year-end adjustment can't handle (large medical expenses, furusato nōzei beyond the one-stop limit, first-year mortgage credit, foreign tax credit). File online via e-Tax or at your local tax office.
OnlineWho: Employee (or a tax accountant, zeirishi)Filing window 16 February - 15 March for the previous yearFree to self-file; zeirishi fees vary if you hire help
5
Pay residence tax (jūminzei) — billed in arrears from June
Your Tokyo ward calculates jūminzei (~10%: roughly 6% municipal + 4% prefectural, plus a small per-capita levy of about ¥5,000) on LAST year's income. For employees it is normally collected in 12 monthly instalments from your June paycheck (special collection). If you're not on payroll collection, you get vouchers to pay in four instalments (June, August, October, January).
Via employerWho: Ward office assesses; employer deducts monthly (or you pay by voucher)New rate kicks in each June, based on the prior calendar year's income~10% of prior-year taxable income + ~¥5,000 per-capita portion

Documents you’ll need

Residence card (zairyū card) and My Number (Individual Number)
Year-end adjustment declaration forms from your employer (dependents, insurance, basic deduction)
Deduction certificates: life/earthquake insurance, pension/health payments, dependent details
Gensen chōshū-hyō (withholding statement) — needed for any return, loan, or departure filing

Things most newcomers don’t know

Your first jūminzei bill is suspiciously small — and that is the trap.

Because residence tax lags a full year, your first June in Japan you often pay almost nothing (you may not even have been resident the prior 1 January). The shock lands the following June, when the bill reflects a full 12 months of Tokyo salary — set aside ~10% of income in advance.

Source: NTA / PwC — prior-year assessment

Residence tax can chase you after your income drops — or after you leave.

Quitting your job, taking unpaid leave, or flying home doesn't erase a jūminzei bill assessed on last year's earnings. If you were a resident on 1 January, you owe the full year to that ward even if you move on 2 January. Plan a lump-sum payment or a tax agent before you go.

Source: NTA No.12004 (leaving Japan)

In your first years you may be a 'non-permanent resident' — foreign income left abroad is generally not taxed in Japan.

If you've lived in Japan five years or less out of the last ten and aren't a permanent resident for tax purposes, only Japan-source income plus any foreign income you actually remit into Japan is taxable. Remitting overseas savings can convert otherwise-untaxed income into taxable income — time large transfers carefully.

Source: NTA / PwC — residency categories

If you leave Japan mid-year, file your departure return before you go or appoint a tax agent (nōzei kanrinin).

A Japan-resident person or company files and pays on your behalf for both income tax and the lingering residence tax. Without one, a bill can go unpaid after you leave, creating problems if you ever return — submit the 'Notification of Tax Agent' on or before departure.

Source: NTA No.12004

Common mistakes to avoid

Assuming the year-end adjustment covers everything — it does NOT handle medical-expense deductions, furusato-nōzei beyond the one-stop limit, first-year mortgage credit, or a foreign tax credit; those need your own Feb-Mar return.
Budgeting on your first-year take-home pay and getting hit the next June by a jūminzei bill of ~10% of a full year's income.
Leaving Japan without filing a departure return or appointing a tax agent, then ignoring a residence-tax bill already assessed on the prior year.
Missing the ¥200,000 side-income threshold: even small freelance, crypto, or second-job income above ¥200,000 obliges you to file a return the year-end adjustment can't cover.