The association between fetal gender and rare pregnancy complications has not been extensively investigated, and no studies have examined this association in Japanese women. Thus, we used a large Japanese birth registry database to investigate the extent to which fetal gender affects various pregnancy outcomes. We analyzed 1,098,268 women with a singleton delivery with no congenital anomaly at 22 weeks or later between 2007 and 2015. Women carrying a male fetus had a significantly higher risk of placental abruption (adjusted risk ratio [aRR] 1.15, 95% confidence interval (CI) 1.10-1.20)], preterm delivery (aRR 1.20, 95% CI 1.19-1.22), instrumental delivery (aRR 1.27, 95% CI 1.26-1.29), and cesarean delivery (aRR 1.01, 95% CI 1.00-1.02). In contrast, they had a significantly lower risk of preeclampsia (aRR 0.92, 95% CI 0.89-0.94), placenta accreta (aRR 0.90, 95% CI 0.85-0.96), atonic hemorrhage (aRR 0.95, 95% CI 0.93-0.96), and maternal blood transfusion (aRR 0.95, 95% CI 0.92-0.99). Our findings demonstrate a significant association between fetal gender and various pregnancy complications and delivery outcomes among Japanese women.