Summary
If you make 2,639,256 円 a year living in Japan, you will be taxed 510,459 円. That means that your net pay will be 2,128,797 円 per year, or 177,400 円 per month. Your average tax rate is 19.3% and your marginal tax rate is 23.1%. 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 23.11 円, hence, your net pay will only increase by 76.89 円.
Bonus Example
A 1,000 円 bonus will generate an extra 769 円 of net incomes. A 5,000 円 bonus will generate an extra 3,845 円 of net incomes.