Objective: This study examines how the effect of first birth on women’s wages over ten years after childbirth varies by educational attainment in Japan and how the loss of work experience contributes to the penalty. Background: Studies have examined whether higher educational attainment protects women from the motherhood wage penalty. However, the results are inconsistent and there is little evidence outside the Western context. Furthermore, given the significant role of experience loss following childbirth, this may contribute to educational differences in the motherhood wage penalty. Method: Event study models with fixed effects are employed to the Japanese Panel Survey of Consumers, a nationally representative panel survey data covering the period 1993–2021. Results: The negative effect of motherhood increases with years regardless of educational group, with no significant educational differences. Moreover, the loss of experience significantly mediates most of the negative effects. While highly educated women are less likely to interrupt their employment, they face a significant wage penalty due to the larger negative effect of experience loss. Conclusion: This study provides evidence on educational differences in the motherhood wage penalty and the role of loss of experience in Japan. The results suggest that the balance between the likelihood of employment interruption and its negative effect influences the direction of the educational gradient in the motherhood wage penalty in general.