Objectives Female genital mutilation/cutting (FGM/C) is a surgical intervention that is still widely performed around the world with serious obstetric and neonatal outcomes. We aimed to determine the obstetric and neonatal effects of FGM/C in pregnant women in a hospital with high standards of care in Sudan, where this is a common case, using a homogenous patient group. Methods This is a retrospective cohort study in pregnant women with FGM/C, conducted at Nyala, Sudan-Turkey Training and Research Hospital. The inclusion criteria were: >18 years of age, history of FGM/C, vertex presentation, full-term birth, and single pregnancy. FGM/C group was compared with women without FGM/C (control group) who were monitored for the same period of 8 months in terms of age, parity, gestational age, and obstetric and neonatal outcomes. Results A total of 220 eligible pregnant women were included in the study. Each group consisted of 110 pregnant women (FGM/C and control groups). We noticed that in the FGM/C group more emergency C-sections occurred, the second stage of the delivery was prolonged significantly, and episiotomy and periclitoral injuries were higher. Also, it was seen that postpartum blood loss and hospitalization of the mother lasted longer in the FGM/C group. No significant differences were found between the two groups with regard to newborns. Conclusions FGM/C is definitely associated with poor obstetric outcomes. These patients should be diagnosed during the antenatal period, and the delivery processes should be managed by experienced healthcare professionals according to the type of FGM/C.