By using unique data about academic economists in Japanese universities, we conduct the first detailed study of gender salary differences within Japanese academia. Despite the common belief among Japanese academics that there cannot be a gender salary gap within the Japanese academia, our empirical results show that female academic economists earn 7% less than comparable males, after controlling for rank and detailed personal, job, institutional and human capital characteristics. The coefficient for the female dummy has almost the same value, regardless of whether rank is included or excluded from the salary equation, suggesting that there is a significant gender salary gap within each rank, but there are no gender differences in rank attainment. Our results contrast with findings from previous studies in the US and in the UK where most of the gender salary differences stem from rank attainment differences. We provide possible explanations for why our results are different. Refereed articles, the most commonly accepted measures of productivity, have no statistically significant effect on salary. The fixed-term employment is associated with 24% lower annual salary and private university has a salary premium of 16%.