Follicle-stimulating hormone receptor (FSHR) is an important G protein-coupled receptor, which is required for steroidogenesis, follicular development and female infertility. Here, we report a novel polymorphism in the 3'-UTR that strongly influences ovine FSHR mRNA decay. The partial 3'-UTR sequence of Hu sheep FSHR gene was isolated and characterized, and a polymorphism (c.2327A>G) was identified. Luciferase assay and qRT-PCR showed that c.2327A>G polymorphism in the 3'-UTR exerts a strong regulatory role in FSHR transcription. This regulatory role is achieved by affecting FSHR mRNA decay. Furthermore, the c.2327A>G mutation in the 3'-UTR influences ARE (AU-rich element, a cis-acting element promoting mRNA decay)-mediated mRNA decay of Hu sheep FSHR gene. Together, our study identified a novel polymorphism and elucidated a new mechanism underlying transcriptional regulation of FSHR in mammals.