Cell junctions are the sites at which cells attach to the neighboring cells. They do not only maintain tissue integrity, their turnover also plays a crucial role in cell development and morphogenesis. In the testis, tight junctions and adherens junctions are dynamically remodeled to allow the movement of post-meiotic germ cells across the seminiferous epithelium and the timely release of spermatids into the tubular lumen. There is growing evidence that this dynamic remodeling of cell junctions is mediated by several mechanisms at the transcriptional and post-translational levels. This review summarizes what is known about the transcriptional regulation, ubiquitination and endocytosis that are involved in modulating junction dynamics in epithelial cells. It also highlights the recent findings on the regulation of junction dynamics in the testis and the specific areas that require further research for a thorough understanding of the role of junction remodeling in spermatogenesis. Understanding the junction dynamics in the seminiferous epithelium may unfold new targets for non-hormonal male contraceptive development.