Exercise can increase neurogenesis and affect gene expression in the brains of adult rats. Little is known about how exercise intensity affects neurogenesis and associated gene expression in juvenile rats. Here, we show that exercise influenced neurogenesis and mRNA expression of brain derived neurotrophic factor (BDNF), N-methyl-d-aspartate receptor type 1 (NMDAR1), vascular endothelial growth factor (VEGF) and fetal liver kinase-1 (Flk-1) in the hippocampus of 5 weeks old rats in an intensity-dependent manner. One week of low- or moderate-intensity exercise in a treadmill running task enhanced neurogenesis in the dentate gyrus of hippocampus. The low-, but not the high-, intensity exercise paradigm resulted in significantly increased expression of BDNF, NMDAR1, and Flk-1 mRNA. Gene expression levels in the low-intensity exercise group were greater than the high-intensity group for these four molecules.