Summary
If you make 90,599,600 円 a year living in Japan, you will be taxed 37,705,587 円. That means that your net pay will be 52,894,013 円 per year, or 4,407,834 円 per month. Your average tax rate is 41.6% and your marginal tax rate is 46.1%. This marginal tax rate means that your immediate additional income will be taxed at this rate. For instance, an increase of 100 円 in your salary will be taxed 46.10 円, hence, your net pay will only increase by 53.90 円.
Bonus Example
A 1,000 円 bonus will generate an extra 539 円 of net incomes. A 5,000 円 bonus will generate an extra 2,695 円 of net incomes.