In 2005, the Ministry of Health in Rwanda, with the support of the Belgian Technical Cooperation, launched a strategy of performance-based financing (PBF) in a group of 74 health centres (HCs), covering 2-m inhabitants. In 2006, PBF was extended to an additional group of 85 HCs, thus reaching 3.8-m inhabitants. This study evaluates the effect of PBF on HC performance from 2005 to 2007. Composite indicators for measuring quantity and quality of services were developed and evaluated through monthly formative supervisions by qualified and well-trained district supervisors. The strategy was based on a fixed fee per quality-approved service. The entire budget spent on the implementation of PBF amounted to $0.25/cap/year, of which $0.20/cap/year for subsidies and an estimated $0.05/cap/year for administration, supervision and training. A positive effect on utilization rates was only seen for activities that were previously less well organized; in this case, growth monitoring services and institutional deliveries. The quality of services, defined as the compliance rate with national and international norms, rose considerably for all services in both groups. A sustained level of quality between 80% and 95% was reached within 18 months in the first group. A similar result was reached in the second group in 8 months.