Summary
If you make 3,890,748 円 a year living in Japan, you will be taxed 809,937 円. That means that your net pay will be 3,080,811 円 per year, or 256,734 円 per month. Your average tax rate is 20.8% and your marginal tax rate is 28.9%. 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 28.90 円, hence, your net pay will only increase by 71.10 円.
Bonus Example
A 1,000 円 bonus will generate an extra 711 円 of net incomes. A 5,000 円 bonus will generate an extra 3,555 円 of net incomes.