Summary
If you make 3,923,880 円 a year living in Japan, you will be taxed 819,511 円. That means that your net pay will be 3,104,369 円 per year, or 258,697 円 per month. Your average tax rate is 20.9% 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 28.89 円, hence, your net pay will only increase by 71.11 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 3,556 円 of net incomes.