Prostatitis plays a major role in morbidity and mortality related to prostate diseases. The aim of this study was to detect whether thymoquinone (TQ) could ameliorate oxidative damage and the proliferative response induced by Escherichia coli (E. coli) in rats. A total of 42 adult male Wistar rats were used. The rats were randomly divided into seven groups (three treatment groups, three infected groups and one control group). Control group received saline and was killed 24 h after saline administration. Infected rats were killed after 24, 48 and 72 h following direct injection of E. coli into the prostate. Treatment groups were administered with 10 mg/kg dose of TQ intraperitoneally following E. coli injection and after 24 and 48 h following E. coli injection. The rats were killed at 24, 48 and 72 h after the first drug administration. Each group was compared with each other and with the control group. In addition, infected groups were compared with treatment groups. Our findings show that the treatment with TQ has a protective effect against bacterial prostatitis-induced tissue injury. Increase in malondialdehyde levels and histological damage caused by E. coli were improved markedly with TQ treatment. TQ treatment particularly increased the activity of glutathione peroxidase and decreased the activities of catalase and superoxide dismutase. These observations might be attributed, at least in part, to the antioxidant effect of TQ and suggest that it could be a clinically valuable agent in the prevention of acute prostatitis caused by E. coli.