Follicle-stimulating hormone (FSH) is necessary for fertility in both sexes as a regulator of gametogenesis and hormone synthesis. Humans with loss-of-function mutations within the gene encoding the FSH beta subunit (FSHB) are infertile. Similarly, female Fshb knock-out mice are infertile and fail to ovulate, and males are subfertile. We recently reported the discovery and characterization of an upstream enhancer of FSHB located 26 Kb upstream of the transcriptional start site in humans (-17 Kb in mouse) that also amplifies activin and gonadotropin-releasing hormone induction of FSHB. Notably, the upstream enhancer contains a polymorphic, fertility-associated site in humans, rs11031006 (G/A), and the minor allele (A) increased enhancer activity in vitro as compared to the major allele (G), likely by increasing the affinity of an SF1 binding element. To investigate the role of the novel enhancer and rs11031006 variant in vivo, we created mouse models to assess deletion of the upstream enhancer and the impact of the G>A point mutation at the rs11031006-equivalent base. A full characterization of the -17 Kb enhancer deletion model revealed no apparent differences in fertility or serum FSH/LH levels, nor did a larger deletion that also included an additional putative regulatory element. In contrast, female mice homozygous for the mutated A allele at the rs11031006-equivalent position had fewer litters over a 120-day fertility assay, abnormal estrous cycling at 10 months, and reduced pituitary Lhb transcript abundance. Overall, while the mouse -17 Kb Fshb enhancer is dispensable for fertility, the rs11031006-equivalent G>A mutation results in subfertility in females.