The study estimated the user cost of Caesarean section (CS), a major component of emergency obstetric care (EmOC), in a post conflict situation in Bunia, DR Congo, 2008. A case control study used a structured questionnaire to compare women who had a CS (cases) with women who had a vaginal delivery (controls). Service information was recorded in 20 facilities providing obstetric care. Maternal and perinatal deaths, including those outside health facilities, were recorded and verified. The user cost of CS was estimated at four hospitals, one of them managed by an international non‐governmental organization offering EmOC free of charge, compared to the user cost of women who had a vaginal delivery. Among paying users, the mean healthcare cost was $US68.0 for CS and $US12.1 for vaginal delivery; mean transport cost to and from the hospital was $US11.7 for cases and $US3.2 for controls. The mean monthly family income was $US75.5. The user cost of CS placed an important financial burden on patients and their families. During transition from humanitarian to developmental assistance, donors and the State should shore up the EmOC budget to avoid an increase in maternal and perinatal mortality. Copyright © 2013 John Wiley & Sons, Ltd.