AimSurgical site infection (SSI) is one of the most common postoperative complications in gastrointestinal surgery. To clarify the superiority of 1.5% olanexidine, we conducted a randomized prospective clinical trial that enrolled patients undergoing gastrointestinal surgery with operative wound classes II–IV.MethodsTo evaluate the efficacy of 1.5% olanexidine in preventing SSIs relative to 10% povidone‐iodine, we enrolled 298 patients in each group. The primary outcome was a 30‐day SSI, and the secondary outcomes were incidences of superficial and deep incisional SSI and organ/space SSI. In addition, subgroup analyses were performed.ResultsThe primary outcome of the overall 30‐day SSI occurred in 38 cases (12.8%) in the 1.5% olanexidine group and in 53 cases (18.0%) in the 10% povidone‐iodine group (adjusted risk ratio: 0.716, 95% confidence interval: 0.495–1.057, p = 0.083). Organ/space SSI occurred in 18 cases (6.1%) in the 1.5% olanexidine group and in 31 cases (10.5%) in the 10% povidone‐iodine group, with a significant difference (adjusted risk ratio: 0.587, 95% confidence interval: 0.336–0.992, p = 0.049). Subgroup analyses revealed that SSI incidences were comparable in scheduled surgery (relative risk: 0.809, 95% confidence interval: 0.522–1.254) and operative wound class II (relative risk: 0.756, 95% confidence interval: 0.494–1.449) in 1.5% olanexidine group.ConclusionOur study revealed that 1.5% olanexidine reduced the 30‐day overall SSI; however, the result was not significant. Organ/space SSI significantly decreased in the 1.5% olanexidine group. Our results indicate that 1.5% olanexidine has the potential to prevent SSI on behalf of povidone‐iodine.