For the purpose of investigating the role of physical exercise in developmental seizure-induced cognitive deficit, hippocampal mossy fiber sprouting and related gene expression, a seizure was induced by penicillin every other day in Sprague-Dawley rats from postnatal day 24 (P24). The authors assigned ten rats each randomly into the control group (CONT1), the control plus exercise group (CONT2), the seizure group (EXP1) and the seizure plus exercise group (EXP2). Morris water maze test was used respectively during P39-P45 and P61-P66. Treadmill exercise was performed daily by CONT2 and EXP2 rats during P49-P54. On P66, mossy fiber sprouting and gene expression in hippocampus were assessed by Timm staining and real-time RT-PCR. EXP2 rats performed better than EXP1 rats in the second water maze navigation test. In the entire two spatial probe tests, both EXP1 and EXP2 rats performed worse than the two control rats. Physical exercise remarkably reduced the aberrant mossy fiber sprouting in the supragranular region of dentate gyrus and CA3 subfield of hippocampus. Both EXP1 and EXP2 rats had a higher amount of glutamate receptor 1 (GluR1) and lower amount of the ratio of GluR2/GluR1 in hippocampus when compared with CONT rats. In addition, there was long-term enhancement of both gamma-aminobutyric acid receptor A-alpha3 (GABA-Aalpha3) and cholecystokinin (CCK) of EXP2 rats compared with the other three groups. These results showed that physical exercise improved learning capacity by modulating hippocampal regenerative sprouting and related gene expression in a developmental rat model of penicillin-induced recurrent epilepticus.