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Objective: To determine the effectiveness of povidone‐iodine application after skin closure to prevent surgical site infection after an emergency cesarean section and to assess risk factors associated with surgical site infection. Methods: A randomized controlled trial enrolled 352 pregnant women who required emergency cesarean delivery at King Chulalongkorn Memorial Hospital, from August 2018 to March 2019. Participants were randomly assigned to receive the povidone‐iodine application at the incision after skin closure (n = 176) or without application (n = 176). Thirty‐day surveillance of complications and adverse effects was performed. The primary outcome was the incidence of surgical site infection, which was compared between groups using the chi‐squared test. The adjusted odds ratios (ORs) of the factors associated with surgical site infection were determined by logistic regression analysis. Results: There were no significant differences in the incidence of surgical site infection and adverse effects between the povidone‐iodine and control groups (9.5% vs 7.1%, P = 0.430). The significant factor associated with surgical site infection was a long interval (≥60 min) from the administration of prophylactic antibiotics to the incision (adjusted OR 4.06, 95% CI 1.49–11.03). Conclusion: The application of povidone‐iodine after skin closure in an emergency cesarean section did not have the advantage of reducing the incidence of surgical site infection. Clinical Trial Registration: This study was registered in TCTR registry on March 10, 2018 with trial identification number: TCTR20180310002 (https://www.thaiclinicaltrials.org/show/TCTR20180310002). The first participant was recruited on August 2, 2018. Synopsis: Application of povidone‐iodine on skin incision after closure in emergency cesarean section did not provide an advantage in reducing the incidence of surgical site infection. [ABSTRACT FROM AUTHOR]