Summary
If you make 5,061,684 円 a year living in Japan, you will be taxed 1,175,955 円. That means that your net pay will be 3,885,729 円 per year, or 323,811 円 per month. Your average tax rate is 23.2% 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.