In rodents, daily maternal separation for 180 min (MS180) during the first weeks of life affects hippocampal granule cell neurogenesis. Development of the cerebellum granule cell layer also occurs during the first weeks of life. However, whether MS180 affects this neurogenic niche remains unknown. To study this, we evaluated the immediate and long term effect of MS180 on granule cell survival within the cerebellum. Pups were injected twice at an 8-hour interval at PND (postnatal day) 5 with bromodeoxyuridine (BrdU, 50 mg/kg) and were sacrificed ten days later (PND15) or allowed to survive into adulthood (PND60). We observed a higher density of BrdU-positive cells in the cerebellar foliae (p < 0.05) of MS180 pups at PND15. This increase was also observed in both, cerebellar foliae and fissures (p < 0.05) at PND60. Triple immunofluorescence staining against BrdU, NeuN (a marker of mature neurons), and GFAP (a marker of mature glia), revealed that BrdU + cells labeled at PND5 co-localized with NeuN but not with GFAP, indicating that they were mature neurons. MS180 did not affect baseline corticosterone levels at PND15 but significantly increased adult corticosterone levels (p < 0.05). In conclusion, MS180 increased cell survival in the granular layer of cerebellar foliae and fissures and resulted in further integration of the cells into adult circuits. These effects occurred without early alterations of basal corticosterone by MS180. Our results indicate that early-life stress induces a permanent increase in cerebellar neurogenesis.