The acidic luminal environment of the epididymis is regulated by the communication networks among epididymal epithelial cells; it is necessary for sperm maturation and storage. To characterize epididymal epithelial cell differentiation, the localization and expression of hydrogen-pumping vacuolar ATPase (V-ATPase) and cytokeratin 5 (KRT5) in the clear and basal cells, respectively, of immature and mature goat epididymis and vas deferens was examined. The epididymides and vas deferens were obtained from goats aged 1, 2, and 12–14 months. To assess the localization and expression patterns of V-ATPase and KRT5 in the caput, corpus, and cauda of the epididymis and proximal vas deferens, the tissue sections were subjected to immunofluorescence labeling and observed by confocal microscopy. Both clear and basal cells progressively started to differentiate in a retrograde manner. Clear cells disappeared from the cauda region after puberty, and they were maintained only in the caput and corpus regions of the adult goat epididymis. V-ATPase and KRT5 were co-expressed in the differentiated cells located at the base of the epithelium (i.e., basal cells). This cell type-specific differentiation and distribution of the epithelial cells plays a critical role in establishing a unique luminal environment for sperm maturation and storage in the goat epididymis.