46,XY gonadal dysgenesis (GD) is a Disorder/Difference of Sex Development (DSD) that can present neonatally as ambiguous genitalia or at puberty as a phenotypic female lacking secondary sexual characteristics and primary amenorrhea. Only 43% of 46,XY DSD cases receive a molecular diagnosis. In mice, Fibroblast growth factor 9 (FGF9) is an important component of the male sex-determining pathway. While pathogenic FGF9 variants that cause skeletal defects in humans show gonadal alterations in mouse models, a role for FGF9 in human testicular development is not known. Here, we describe an FGF9 missense variant, NM_002010.2:c.583G>A:p.(Asp195Asn), in a female patient with isolated 46,XY GD. Using biochemical and cell-based approaches, we demonstrate that the D195N variant disrupts FGF9 protein homodimerisation and FGF9-heparin-binding, reducing Sertoli cell proliferation. XY Fgf9D195N/D195N mice showed a mild gonadal phenotype (disrupted testis cords), while XY Fgf9D195N/- mice showed male-to-female sex reversal (ovotestis). The incomplete penetrance and variable expressivity of the D195N variant in mice suggested an oligogenic basis for the patient's DSD. Further detailed analysis of the patient and parental exome revealed variants in genes expressed in human embryonic Sertoli cells at the time of sex determination, which may contribute to the gonadal anomalies. Our findings therefore suggest that disruption to FGF9 signaling may, in combination with other variants, compromise human testis determination and lead to 46,XY DSD.