In this study, 32 male Sprague–Dawley rats (8 for each group) were used in total to examine the effects of valproic acid on rat cerebellum. It was determined that the experimental group received valproic acid (600 mg/kg) on embryonic day 15 and postnatal day 11, whereas the control group was treated with saline on the same days. Moreover, on the postnatal 30th day, the cerebellums of all pups were removed and prepared for light and electron microscopy. The numerical density of granule cells in the cerebellum of experimental groups of rats increased, whereas the numerical density of Purkinje cells decreased. Furthermore, the granule cells had a smaller mean nuclear diameter in one of the experimental groups, while the Purkinje cells had in both experimental groups than those in the comparison group. Thus, the numerical density of synaptic disks and their mean diameter in the cerebellar granular layer of experimental groups were significantly decreased compared to the corresponding controls; also, the synapse‐to‐neurons ratio, a parameter indicating interneural connectivity, was the same. Consequently, it was seen that valproic acid administration to pups in prenatal or early postnatal days causes changes in number of neurons and synapses in the cerebellum of rats.