Reproductive seasonality in Neotropical bats has been assessed to the better understand their reproductive behavior. This knowledge is especially important for the control of Desmodus rotundus population as it is a transmitter of rabies virus. Therefore, we aimed to evaluate the functional activity of testis and epididymis of D. rotundus in dry and rainy seasons under a morphological approach. We observed an increase in tubular diameter and epithelial height of the seminiferous tubules during the rainy season. In the latter, additionally, stereological analysis of the testis showed increased proportion of seminiferous epithelium and reduced percentage of lumen. The sperm number in caput/corpus epididymis increased in rainy season, whereas sperm count and transit time were reduced in cauda region. These alterations were probably related to the recovery of epithelium activities after mating season in dry season. Despite altered nuclear and cytoplasm parameters of Leydig cells between seasons, the volume and number of these cells were constant. Moreover, no change in serum testosterone levels, daily sperm production, and apoptotic index were observed, which indicates that the reproductive pattern in D. rotundus does not change between seasons. Our study offers a baseline for the management of vampire bat population as an attempt to control rabies disease.