Resident tax runs on a one-year delay by design, not by accident. Your city or ward tax office totals up everything you earned in a calendar year, then bills you for it starting the following June, withheld from your payslip in 12 monthly installments through the May after that. So the resident tax line on any given payslip has nothing to do with what you're earning right now, it's settling up on a year that already finished.
The rate itself is a flat 10% of the same taxable income base used for national tax, split roughly 6% municipal and 4% prefectural. On top of that, nearly everyone pays a small flat per-capita charge of about ¥6,000 a year, which folds in a municipal share, a prefectural share, and a national forest environment tax collected alongside it since FY2024.
This timing gap is exactly why a first year in Japan can feel deceptively light on resident tax, and why the bill that shows up in year two on an unchanged salary catches people off guard. It also matters in reverse: if you leave Japan or take a pay cut, you're still on the hook for resident tax based on the higher income you earned the year before, since that liability was already locked in.