Background In Japan, there is a large geographical maldistribution of obstetricians/gynecologists, with a high proportion of females. This study seeks to clarify how the increase in the proportion of female physicians affects the geographical maldistribution of obstetrics/gynecologists. Methods Governmental data of the Survey of Physicians, Dentists and Pharmacists between 1996 and 2016 were used. The Gini coefficient was used to measure the geographical maldistribution. We divided obstetricians/gynecologists into four groups based on age and gender: males under 40 years, females under 40 years, males aged 40 years and above, and females aged 40 years and above, and the time trend of the maldistribution and contribution of each group was evaluated. Results The maldistribution of obstetricians/gynecologists was found to be worse during the study period, with the Gini coefficient exceeding 0.400 in 2016. The contribution ratios of female physicians to the deterioration of geographical maldistribution have been increasing for those under 40 years and those aged 40 years and above. However, there was a continuous decrease in the Gini coefficient of the two groups. Conclusions The increase in the contribution ratio of the female physician groups to the Gini coefficient in obstetrics/gynecology may be due to the increased weight of these groups. The Gini coefficients of the female groups were also found to be on a decline. Although this may be because the working environment for female physicians improved or more female physicians established their practice in previously underserved areas, such a notion needs to be investigated in a follow-up study.