During the Drosophila oogenic processes, Fat facets (Faf), an ubiquitin-specific protease essential for normal development of oocyte and eye, becomes localized at the posterior pole and is incorporated into the pole cells. This is dependent on Oskar, a key factor for pole cell determination, and suggests a role for Faf in germ cell differentiation and development. Here we show that Usp9x, an X-linked ortholog of Faf, is predominantly expressed in both germ cell and supporting cell lineages during mouse gonadal development in stage- and sex-dependent manners. Usp9x was first detected in PGCs at 10.5 days post coitum (dpc), and thereafter its expression both at mRNA and protein levels was enhanced in PGCs of both sexes at 11.5–13.5 dpc. In testis, Usp9x expression rapidly decreased to an undetectable level by 15.5 dpc and after birth to adult, no expression was found in any spermatogenic cells, except for weak expression in Sertoli cells. In the ovary, Usp9x expression in embryonic oocytes was also reduced at the newborn stage, its expression reappeared in oocytes at secondary follicle stage, and its products were highly accumulated in the cytoplasm of Graaffian follicles in adults. Although follicular epithelial cells also expressed Usp9x at a moderate level during postnatal development, its expression was downregulated from early secondary follicle stage. Thus, the present study is not only the first to demonstrate a conserved expression of fat facets in PGCs between mouse and fly, but also sex- and stage-dependent changes of a specific component of the deubiquitylation system during mammalian gonadal development.