Background: Cesarean sections are among the most common obstetric procedures performed globally. The rate of cesarean section and its post-operative complications are also increasing.2 One of the post operative complications is surgical site infection. Preventing or reducing the incidence of SSI can improve patient outcomes. It is feasible to lower post-operative infections by employing skin antisepsis prior to surgery, which includes the use of chlorhexidine alcohol and povidone-iodine alcohol. Objective: To compare the efficacy of chlorhexidine alcohol versus povidone iodine alcohol for pre-operative skin preparation for prevention of surgical site infection in cesarean section. Methods: A comparative, cross-sectional study was conducted at Department of Obstetrics & Gynecology, KRL Hospital, Islamabad. From September 2025 to November 2025. Pregnant women between the ages of 18 and 45 who were booked for a cesarean section were included in the study. Patients with a skin infection at the operation site, those who had taken steroids for longer than two weeks in the preceding two months, women who are known diabetics, and those who were allergic to alcohol, povidone iodine, or chlorhexidine were excluded. The lottery approach was then used to divide the patients into two groups, A and B, each consisting of 47 cases. Patients in Group A received chlorhexidine alcohol, for pre-operative skin preparation during cesarean sections, while women in Group B received povidone iodine. A weekly follow-up was carried out for 30 days after discharge, or as soon as symptoms of a wound infection appeared. Results: The average age of the women in groups A and B was 27.77 ± 4.55 and 27.00 ± 5.63 years, respectively. The mean gestational age was 38.67 ± 1.04 weeks, with a range of 35 to 40 weeks. The mean parity was 2.11 ± 1.04. The incidence of surgical site infection in patients having cesarean sections was 04 (8.51%) and 11 (23.40%) for chlorhexidine alcohol and povidone iodine, respectively (p-value = 0.049). Conclusion: This study shows that pre-operative skin preparation using chlorhexidine alcohol reduces SSI more effectively than povidone iodine.