The antibiotic treatment rate of chronic bacterial prostatitis (CBP) is low, and long-term administration can result in adverse events and bacterial resistance. For these reasons, a new preventive modality, which can replace traditional antibiotic therapy, is required. To evaluate the preventive effect of selenium on CBP, the pre-treatments were divided into four groups, administered for 4 weeks, as follows: (1) control, (2) ciprofloxacin, (3) selenium, and (4) ciprofloxacin and selenium. Then, drip infusion of a bacterial suspension (Escherichia coli Z17, O2:K1; H-) into the prostatic urethra of Wistar rats was conducted to induce CBP. In 4 weeks, the results of microbiological culture of prostate and urine samples as well as histological findings of the prostate in each group were analyzed. Selenium decreased bacterial infection significantly; the decrease in infiltration rate of inflammatory cells into prostate tissues in the selenium group was similar to that in the control group. The effect of hindering bacterial infection on prostate tissue was greater in the group administered both selenium and an antibiotic than in other groups given only one of the agents. Although the findings of this study suggest that selenium can have a preventive effect against the occurrence of CBP, methods to prevent CBP are still controversial.