Background: Since 2011, Benin adhered to results-based financing (RBF), with the implementation of RBF_PRPSS model by Health System Performance Strengthening Project (PRPSS) and RBF_PASS model by health system support project (PASS). Notwithstanding the lack of evidence on this experimental phase, the Ministry of Health initiated the extension of the RBF_PRPSS model to uncovered areas. This comparative study was led to evaluate the health system performance in RBF zones.Methods: The study examined data from sixty-seven health facilities in six health zones offering maternal and child health services, using the double difference, the Student's test and the variance comparison, with 5% significance level.Results: The study found that between 2011 and 2014, staff numbers remained stable in the RBF strata (p>0.05). The cumulative duration over a six-month period of stock-outs of five key drugs (paracetamol, amoxicillin, oxytocin, iron, sulfadoxine pyrimetamine) decreased from 51 days to 29 days (p<0.05). Direct revenues per health facility increased more in the RBF strata (p<0.05). Financial viability increased in RBF_PRPSS stratum. Health services utilization improved significantly for institutional delivery, tetanus toxoid immunization, DTP (Hib) HepB 3 and MCV immunization and curative care. Decreasing of maternal and neonatal mortalities in RBF strata were not significant.Conclusions: In sum, the RBF implementation has not yet generated a significant effect on the overall performance of the health system in exposed areas, although it is already accompanied by a significant improvement in the utilization of certain health care services.