Both epidemiologic and laboratory studies suggest that parents can shape their offspring's development. Recently, it has been shown that maternal exercise during pregnancy benefits the progeny's brain function. However, little is known regarding the influence of paternal exercise on their offspring's phenotype. In this study we attempt to determine the effects of 6 weeks paternal treadmill exercise on spatial learning and memory and the expression of brain-derived neurotrophic factor (BDNF) and reelin in their male offspring. Sibling males were divided into two groups: the control (C) and the exercise group (E). The mice in the E group were exercised on a motor-driven rodent treadmill for 5 days per week for 6 weeks. After 6 weeks of exercise, the male mouse was mated with its sibling female. After weaning, male pups underwent behavioral assessment (Open field and Morris water maze tests). Immunohistochemistry staining, real time-PCR and western blot were performed to determine hippocampal BDNF and reelin expression of the male pups after behavior tasks. Our results showed that paternal treadmill exercise improved the spatial learning and memory capability of male pups, which was accompanied by significantly increased expression of BDNF and reelin, as compared to those of C group. Our results provide novel evidence that paternal treadmill exercise can enhance the brain functions of their F1 male offspring.