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Objective To investigate the factors associated with Cesarean section (CS) in Bhutan. Methods This was a cross-sectional study, using the retrospective data from the birth registers maintained in comprehensive EmOC (emergency obstetric care) centers for the year 2018. The data was entered in excel 2013 and analyzed using STATA 13. Multiple logistic regression was used to understand the factors associated with CS in Bhutan. Results The rate of CS in Bhutan was 18.7%. The indications of CS were previous CS, fetal distress, prolonged labor and failed induction. The factors associated with CS were maternal age > 25 years, male child, women with lesser number of living child, multiple pregnancy and gestation period > 40 weeks. In addition, mothers delivering in Samtse hospital and Central Regional Referral Hospital had higher odds of CS. Conclusion In Bhutan, the CS was commonly performed for mothers with previous CS, fetal distress and prolonged labor. Increasing maternal age, multiple pregnancy and postdated pregnancy and those with one or lesser number of live children were more likely to undergo CS. To reduce the CS rate, Bhutan should focus on decreasing the primary CS as well as prevent over diagnosis of prolonged labor by focusing on partograph.