Snakes exhibit considerable variation in reproductive patterns. However, the cycle of the sexual segment of the kidney and the testicular activity remain unknown for most Neotropical snake species. The dipsadine Atractus pantostictus is a fossorial snake species occurring in central and southeastern Brazil. The present study describes the reproductive cycle of males of this species, providing macroscopic and microscopic analyses of testes, ductus deferens, and sexual segment of the kidneys. We classified the cycle of males as pre-nuptial, as the production of gametes in males precedes the mating season. In summer, the specimens underwent testicular regression; thus, the individuals of A. pantostictus presented a discontinuous cyclical pattern in which the gonads or accessory organs become reproductively quiescent for some period during the year. At the population level, our results indicated a seasonal reproductive cycle. The sexual segment of the kidney was hypertrophied during the spring, corresponding to the mating season.