BackgroundIn Ethiopia, female genital mutilation (FGM) remains a serious concern and has affected 23.8 million women and girls, with the highest prevalence in Somali regional state. Even though FGM is reported to be associated with a range of obstetric complications, little is known about its effects on childbirth in the region. Therefore, the objective of this study was to test the hypothesis that FGM is a contributing factor to the increased risk of complication during childbirth.MethodsFacility based cohort study, involving 142 parturients with FGM and 139 parturients without FGM, was conducted in Jijiga town from October to December, 2014. The study participants were recruited by consecutive sampling technique. Data were collected using a structured interviewer administered questionnaire and observational checklists. Data were analyzed using SPSS version 16 and STATA version 11.ResultsThe existence of FGM was significantly associated with perinealtear [RR = 2.52 (95% CI 1.26–5.02)], postpartum blood loss [RR = 3.14 (95% CI 1.27–7.78)], outlet obstruction [RR = 1.83 (95% CI 1.19–2.79)] and emergency caesarean section [RR = 1.52 (95% CI 1.04–2.22)]. FGM type I and FGM type II did not demonstrate any association with prolonged 2nd stage of labour, emergency caesarean section, postpartum blood loss, and APGAR score < 7. FGM type III however was significantly associated with prolonged 2nd stage of labour [RR = 2.47 (95% CI 1.06–5.76)], emergency caesarean section [RR = 3.60 (95% CI 1.65–7.86)], postpartum blood loss [RR = 6.37 (95% CI 2.11–19.20] and APGAR score < 7 [RR = 4.41 (95% CI, 1.84–10.60)]. FGM type II and type III were significantly associated with perinealtear [RR = 2.45(95% CI 1.03–5.83)], [RR = 4.91(95% CI 2.46–9.77)] and outlet obstruction [RR = 2.38(95% CI 1.39–4.08)], [RR = 2.94(95% CI 1.84–4.71)] respectively.ConclusionWomen with FGM are significantly more likely than those without FGM to have adverse obstetric outcomes. Risks seem to be greater with more extensive form of FGM. Adverse obstetric outcomes can therefore be added to the known harmful immediate and long-term effects of FGM.Electronic supplementary materialThe online version of this article (10.1186/s12884-018-1937-4) contains supplementary material, which is available to authorized users.