Female sexual function disorders (FSFDs) have received less attention than male sexual function disorders, despite being more prevalent. Furthermore, most available literature is on the effect of vaginal delivery (VD) on sexual function, and studies on the effect of caesarean section (CS) are generally lacking. This study determined the comparative effect of CS and VD on FSFDs. A prospective cohort of postnatal mothers at two hospitals in Nigeria was studied. In the intervention group women delivered via CS whereas women in the control group had a VD. Both groups were followed up to 3months to determine the time to first coitus and other FSFs using a validated questionnaire. At 6weeks postpartum, mean time (days) to first coitus was shorter in the CS than in the VD group (29.2 ± 4.3 vs 32.1 ± 4.9; t = 2.38; p = 0.02). However, no difference was observed at 3months (37.3 ± 8.7 vs 40.9 ± 9.9; t = 1.83; p = 0.07). Also, there were no differences in mean Female Sexual Function Index (FSFI) total scores at 6weeks and 3months (p > 0.05). Mean FSFI domain scores at 6weeks for orgasm, satisfaction, and pain were significantly higher in the CS group (p < 0.05). However, there were no differences in any of the domain scores at 3months (p > 0.05). Mode of delivery does not affect time to resumption of coitus after childbirth, and FSF disorders by 3months postpartum. Caesarean section should therefore not be recommended to women merely for early resumption of coital activity or preservation/maintenance of sexual function after childbirth.