This study aimed to investigate the histomorphological and immunohistochemical changes in the ovaries of Small East African goats during the dry and rainy seasons. A total of 180 ovaries were subjected to analysis using hematoxylin and eosin staining and immunohistochemistry for desmin and smooth muscle actin as cytoskeletal components. The results demonstrated the presence of healthy and atretic primordial, primary, secondary, and antral follicles in the ovaries during the dry and rainy seasons. In the dry season, the proportions of healthy primordial, primary, secondary, and antral follicles were 236 (95%), 85 (97%), 25 (78%), and 6 (27%), respectively, whereas the atretic follicles accounted for 12 (5%), 3 (3%), 7 (22%), and 16 (73%). Conversely, during the rainy season, 157 (99%), 61 (98%), 48 (93%), and 31 (92%) were classified as healthy follicles, while 2 (1%), 1 (2%), 4 (7%), and 3 (8%) were categorized as atretic. There was a significant difference in healthy and atretic follicles between the dry and rainy seasons (P < 0.05). Immunohistochemical analysis revealed positive staining for both desmin and smooth muscle actin in the theca cells of secondary and antral follicles, cortical stroma, and tunica media of blood vessels in healthy and atretic follicles during dry and rainy seasons. However, staining was not observed in the granulosa cells and oocytes. Overall, this study indicates that most antral follicles undergo obliterated follicular atresia during the dry season.