The epididymis, a key component of the male reproductive system, controls spermatozoa's maturation, fertility, and storage. The objective of this study is to evaluate the histological, ultrastructural, and immunohistochemical variations in the epididymis of donkeys that occur throughout the year. During the breeding season (spring) and nonbreeding seasons (summer, autumn, and winter), 20 epididymis were collected from adult, clinically healthy donkeys. Compared to non-breeding seasons, the epididymal duct displayed a more active lining epithelium and more sperm in the lumen during the breeding season. The epithelial height is the lowest and the lumen is the widest during the breeding season. Furthermore, the epididymal epithelium in the tail region exhibits undulations with polyps-like projections. The epididymal epithelium is composed mainly of the principal, basal, and dark cells. Tight junction between adjacent principal cells is more obvious in the breeding season as compared to the non-breeding seasons. However, intraepithelial lymphocytes, phagocytic, and other immune cells are more frequent in non-breeding seasons. β-catenin, which is a component of the adherent junctions between adjacent PCs, exhibits more immunoreactivity during the spring. On the other hand, iNOS, an indicator of oxidative stress, reacts positively during the summer. Additionally, during non-breeding seasons, autophagy was detected within the epididymal epithelium which may be linked to stress adaptation. In conclusion, our findings suggest that the histological and ultrastructural characteristics of the epididymal epithelium are more active during spring compared to other seasons of the year.