Using three household surveys, the Japanese Panel Survey of Consumers (JPSC), the Working Person Survey (WPS), and the Survey of Adult Skills (PIAAC), this study estimates the returns to postgraduate education in Japan, considering potential self-selection bias. To mitigate the bias, workers’ undergraduate majors, types of university, and level of cognitive skills are controlled for. These factors explain 6.3–29.2% of the postgraduate wage premium for women, but at most 10.9% for men. Even after controlling for them, the postgraduate wage premium remains positive and significant, ranging from 16.5 to 23.7% for men and 13.5–26.4% for women.