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Abstract Background Despite a significant decrease in maternal mortality in the last decade, Rwanda needs further progress in order to achieve Sustainable Development Goals (SDG)3 which addresses among others maternal mortality. Analysis of severe maternal outcomes (SMO) was performed to identify their characteristics, causes and contributory factors, using standard indicators for quality of care. Methods A prospective case-control study was conducted for which data were collected between November 2015 and April 2016 in four rural district hospitals. The occurrence of SMO with near miss incidence ratios was established, followed by an analysis of the characteristics, clinical outcomes, causes and contributory factors. Results The SMO incidence ratio was 38.4 per 1000 live births (95% CI 33.4–43.4) and the maternal near-miss incidence ratio was 36 per 1000 live births (95% CI 31.1–40.9). The leading causes of SMO were postpartum haemorrhage (23.4%), uterine rupture (22.9%), abortion related complications (16.8%), malaria (13.6%) and hypertensive disorders (8.9%). The case fatality rate was high for women with hypertensive disorders (10.5%; CI 3.3–24.3) and severe postpartum haemorrhage (8%; CI 0.5–15.5). Stillbirth (OR = 181.7; CI 43.5–757.9) and length of stay at the hospital (OR = 7.9; CI 4.5–13.8) were strongly associated with severe outcomes. Conclusions Despite the use of life saving interventions, SMO are frequent. Mortality index was found to be low at the level of district hospitals. SMO were associated with long stay at the hospital and stillbirth. There is a need for improvement of quality of care, referral practices and certain types of infrastructure, especially blood banks, which would ensure truly comprehensive emergency obstetric care and reduce the occurrence of SMO.