Background The relationship between uric acid (UA) and benign prostatic hyperplasia (BPH) is controversial and has rarely been studied in American populations. Methods Data from two cycles of the National Health and Nutrition Examination Surveys, comprising data from 2005 to 2008, were used. The majority of BPH were identified by self-report. We investigated the relationship between UA and BPH using univariate and multivariate logistic regression analyses. Results 2,845 participants were enrolled in the study, including 531 participants with BPH and 2,314 controls. After fully adjusting for all confounders, the risk of developing BPH was reduced by 18% for every 100 μmol/L increase in UA (OR = 0.82, 95% CI: 0.69–0.97, p = 0.023). Participants in the highest quartile of UA were found to have a reduced likelihood of developing BPH (ORQ4vs1 = 0.61, 95% CI: 0.41–0.91) in comparison to those in the lowest quartile of UA. Subgroup analyses found that among those younger than 60 years, non-Hispanic whites, former smokers, heavy drinkers, those without diabetes, or those with hypertension, high UA remained negatively associated with BPH. Conclusions The above results suggest that UA may be a potential protective factor for BPH, but the mechanism needs to be further explored.