The detrimental effects of sleep insufficiency have been extensively explored. However, only a few studies have addressed this issue in adolescents. In the present study, we examined and compared the effects of 72 h paradoxical sleep deprivation (SD) on adolescent (5 weeks old) and adult (~12 weeks old) mice. Following 72 h of SD, induced by a modified multiple-platform method, mice were subjected to behavioral, histological and neurochemical examinations. In both adolescent and adult mice, SD adversely affected short-term memory in a novel object recognition test. Compared with normal-sleep controls, sleep-deprived adolescent mice had an increased density of excitatory synapses in the granule cells of the dentate gyrus, but no such pattern was observed in the adult group. The engulfment of postsynaptic components within the microglia after SD was reduced in adolescents but not in adults, suggesting an impaired microglia-mediated synaptic pruning in adolescent SD mice. Possible contributing factors included the decreases in CX3CR1, CD11b and P2Y12, closely associated with the synaptic pruning via microglial phagocytosis. In adult SD mice, microglia-associated inflammatory reactions were noted. In sum, sleep deprivation induces age-dependent microglial reactions in adolescent and adult mice, respectively; yet results in similar defects in short-term recognition memory. Sufficient sleep is indispensable for adolescents and adults.