Summary
If you make 3,713,904 円 a year living in Japan, you will be taxed 758,841 円. That means that your net pay will be 2,955,063 円 per year, or 246,255 円 per month. Your average tax rate is 20.4% and your marginal tax rate is 23.3%. 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 23.34 円, hence, your net pay will only increase by 76.66 円.
Bonus Example
A 1,000 円 bonus will generate an extra 767 円 of net incomes. A 5,000 円 bonus will generate an extra 3,833 円 of net incomes.