The purpose of this study was to investigate the effects of motor learning on motor function and synaptic plasticity in rats with cerebellar injuries caused by harmaline. The test subjects were divided into three groups, with 15 rats assigned to each group. Group I was a normal control group (induced by saline); Group II was a experimental control group (cerebellar injuries caused by harmaline); Group III was the group that received motor learning after being cerebellar injured by harmaline. In the motor function test, the outcome of group II was significantly lower than that of group III (p<0.001). In the histological findings, the dendrites and nuclei of the cerebellar neurons of the experimental groups were severely damaged. While group III showed a decrease in degeneration of the cerebellar neurons in comparison. The immunohistochemistric response of synaptophysin in the cerebellar cortex was lower in the experimental groups than group I. However group III’s expression of synaptophysin was higher than group II. In electron microscopy findings, the experimental groups showed degeneration of the Purkinje cell. These result suggest that improved motor function by motor learning, after harmaline induced cerebellar injuries, is associated with dynamically altered expression of synaptophysin in the cerebellar cortex and that it is related with synaptic plasticity.