Summary
If you make 5,489,292 円 a year living in Japan, you will be taxed 1,312,172 円. That means that your net pay will be 4,177,120 円 per year, or 348,093 円 per month. Your average tax rate is 23.9% and your marginal tax rate is 31.9%. 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 31.85 円, hence, your net pay will only increase by 68.15 円.
Bonus Example
A 1,000 円 bonus will generate an extra 682 円 of net incomes. A 5,000 円 bonus will generate an extra 3,408 円 of net incomes.