Reproductive failure is a major cause of economic loss and involuntary culling in dairy herds, with endocrine and immunogenetic factors contributing to impaired fertility. FOXP3 modulates regulatory T cells, which play an essential role in maternal immune tolerance during pregnancy. A maternal X-linked FOXP3 variant (g.87298881A>G) has been associated with impaired fertility and reduced anti-Müllerian hormone (AMH) concentrations in cattle; however, its association with reproductive performance and herd stayability remains unclear. This study investigated the associations of the FOXP3 variant with serum AMH concentrations and reproductive performance in Japanese Holstein Friesian cows. A total of 118 lactating cows from two dairy farms in Japan were genotyped using real-time PCR or Sanger sequencing. After excluding one cow that died from an acute condition unrelated to reproductive or production performance, 117 cows (A/A, n = 35; A/G, n = 56; G/G, n = 26) were included in the final analyses. Serum AMH concentrations were measured using an enzyme-linked immunosorbent assay, and reproductive outcomes were monitored during the study period. Serum AMH concentrations did not differ significantly among the three genotype groups. Kaplan-Meier analysis showed a significant difference in time to pregnancy between G/G and A/G cows (P = 0.026), with G/G cows remaining nonpregnant for longer. In the univariate Cox proportional hazards analysis, cows with the FOXP3 risk genotype (G/G) had a lower pregnancy hazard than that of cows with non-risk genotypes (A/A and A/G) (HR = 0.583, 95% CI: 0.343-0.991, P = 0.046). After adjustment for farm and parity, the risk genotype remained significantly associated with a lower pregnancy hazard (adjusted HR = 0.45, 95% CI: 0.26-0.77, P = 0.004). These findings suggest that the FOXP3 risk genotype is associated with impaired reproductive performance, independent of farm and parity. The absence of a significant difference in serum AMH concentrations further suggests that this association cannot be explained solely by differences in ovarian reserve and raises the hypothesis that FOXP3-related immunological mechanisms contribute to the establishment and maintenance of pregnancy.