Several studies have demonstrated the anticonvulsant effect of melatonin. In view of the positive effects of physical exercise in epilepsy, this study analyzed the influence of physical exercise program on the amygdala kindling development in pinealectomized rats. Animals were divided into six groups: pinealectomized rats (PX), sham rats (SHAM), control rats (CTL), pinealectomized rats submitted to an aerobic exercise program (PX ATL), sham rats submitted to an aerobic exercise program (SHAM ATL) and control rats submitted to an aerobic exercise program (CTL ATL). The stimulus parameters consisted of 60 Hz frequency, diphasic square pulses of 1 ms duration applied for 2 s. The mean number of stimulations and the after-discharge (AD) duration for each stage of kindling were similar among CTL and SHAM animals. PX animals showed particular characteristics during kindling development. They did not present stage 1 and spent a shorter time in stage 2 in relation to the CTL and SHAM animals. Consequently, the AD duration and number of stimulations required to reach stage 5 was lower for the PX group when compared to the CTL and SHAM groups. Concerning the exercising groups, CTL ATL and SHAM ATL animals spent a higher time in stage 1 compared to CTL and SHAM groups. Thus, CTL ATL animals also presented a higher number of stimulations in stage 5 compared to CTL animals. The stage 1 not observed in PX animals was present in PX ATL. Consequently, the number of stimulations required to reach stage 5 was statistically higher for the PX ATL group in relation to the PX group. Our results demonstrate that the acceleration in the kindling development of pinealectomized animals can be reverted by physical exercise.