Background Busulfan is an antineoplastic medication that is broadly utilized for cancer treatment. On the other hand, prescription of busulfan may cause sterility in male patients. Therefore, the decrease of this side effect is important. The aim of the present study was to evaluate the effects of ellagic acid on testicular tissue changes, sexual hormones, antioxidant defense system, and caspase-9 and Bcl2 gene expression in the relative sterility rat model following administration of busulfan.Methods Rats were randomly assigned to five groups of 13 animals per group. Sterility was induced by a single injection of busulfan (10 mg/kg) in groups 3, 4 and 5. The control group was not treated. The healthy group received 50 mg/kg ellagic acid. Groups 4 and 5 (treatment group) received 10 mg/kg and 50 mg/kg ellagic acid, respectively for 48 days. Then, the serum levels of antioxidant enzymes, Malondialdehyde, sexual hormones and the testicular damage were evaluated.Results The significant increment of total antioxidant capacity and catalase was seen in both treatment groups (p < 0.001). Also, both treatment groups significantly increased spermatogonia, round spermatids and long spermatids. Treatment with 50 mg/kg ellagic acid significantly increased the testis weight, testis volume, seminiferous tubule volume, germinal epithelium volume, interstitial tissue volume, spermatocyte, Sertoli cells, and Leydig cells in the busulfan group(P < 0.05). Additionally, 50 mg/kg ellagic acid significantly increased the gene expression of Bcl2 and decreased caspase 9 in the busulfan group (P < 0.05).Conclusions The consumption of ellagic acid may have beneficial effects on antioxidant defense system, sexual hormones abnormality and testicular tissue damage.