The free-running circadian period is approximately 30 min shorter in adult male than in adult female Octodon degus. The sex difference emerges after puberty, resulting from a shortened free-running circadian period in males. Castration before puberty prevents the emergence of the sex difference, but it is not a function of circulating gonadal hormones as such, because castration later in life does not affect free-running circadian period. The aim of this study was to determine whether or not the shortening of the free-running circadian period in male degus results from exposure to gonadal hormones after puberty. We hypothesized that masculinization of the circadian period results from an organizational effect of androgen exposure during a post-pubertal sensitive period. Male degus were castrated before puberty and implanted with capsules filled with dihydrotestosterone (DHT), 17β-estradiol (E2) or empty capsules at one of three ages: peri-puberty (2–7 months), post-puberty (7–12 months), or adulthood (14–19 months). Long-term exposure to DHT or E2 did not result in a shortened free-running circadian period when administered at 2–7 or 14–19 months of age. However, E2 treatment from 7 to 12 months of age decreased the free-running circadian period in castrated males. This result was replicated in a subsequent experiment in which E2 treatment was limited to 8–12 months of age. E2 treatment at 7–12 months of age had no effect on the free-running circadian period in ovariectomized females. Thus, there appears to be a post-pubertal sensitive period for sexual differentiation of the circadian system of degus, during which E2 exposure decreases the free-running circadian period in males. These data demonstrate that gonadal hormones can act during adolescent development to permanently alter the circadian system.