Background: Valproic acid-induced autism represents a well-recognized model to induce autism in rats. Bee pollen has potent anti-inflammatory, antioxidant and anti-apoptotic effects. Aim: This work was performed to study the protective effect of bee pollen extract on valproic acid-induced model of autism in rat pups. Materials and methods: The study was performed on 50 male albino rat pups 10-15 gm that were classified into four groups; group 1:control group, group II: rat pups received oral aqueous extract of bee pollen 250 mg/kg once daily from PND 14 to 40, group III: autism was induced by subcutaneous injection of a single dose of valproic acid 400mg/kg on PND 14, and group IV: after induction of autism as in group III, rat pups were treated with an aqueous extract of bee pollen from PND 14 to 40. All rats were sacrificed at PND 41. Cerebellar specimens were processed for histological and immunohistochemical study in addition to morphometric, behavioral and statistical studies. Results: Valproic acid-induced autism group depicted behavioral changes and marked alteration of the histological picture of the cerebellar cortex by light and electron microscopes. A significant decrease in the granular cell layer thickness and a significant increase in the mean area percentage of GFAP immunopositive reaction were observed in group III as compared to the control group. Treatment with Bee pollen showed marked improvement of the previously mentioned pathological changes. Conclusion: Bee pollen could improve the behavioral and histological alterations in the cerebellar cortex of valproic acid-induced autism in rat pups.