To strengthen the health care delivery, the Burundian Government in collaboration with international NGOs piloted performance-based financing (PBF) in 2006. The health facilities were assigned - by using a simple matching method - to begin PBF scheme or to continue with the traditional input-based funding. Our objective was to analyse the effect of that PBF scheme on the quality of health services between 2006 and 2008. We conducted the analysis in 16 health facilities with PBF scheme and 13 health facilities without PBF scheme. We analysed the PBF effect by using 58 composite quality indicators of eight health services: Care management, outpatient care, maternity care, prenatal care, family planning, laboratory services, medicines management and materials management. The differences in quality improvement in the two groups of health facilities were performed applying descriptive statistics, a paired non-parametric Wilcoxon Signed Ranks test and a simple difference-in-difference approach at a significance level of 5%. We found an improvement of the quality of care in the PBF group and a significant deterioration in the non-PBF group in the same four health services: care management, outpatient care, maternity care, and prenatal care. The findings suggest a PBF effect of between 38 and 66 percentage points (p<0.001) in the quality scores of care management, outpatient care, prenatal care, and maternal care. We found no PBF effect on clinical support services: laboratory services, medicines management, and material management. The PBF scheme in Burundi contributed to the improvement of the health services that were strongly under the control of medical personnel (physicians and nurses) in a short time of two years. The clinical support services that did not significantly improved were strongly under the control of laboratory technicians, pharmacists and non-medical personnel.