Performance-based financing (PBF) is a mechanism by which health providers are paid on the basis of outputs or results delivered. A PBF program was implemented on the provision of HIV, prevention of mother-to child HIV transmission (PMTCT), and maternal/child health (MCH) services in two provinces of Mozambique. A retrospective case-control study design was used in which PBF provinces were matched with control provinces to evaluate the impact of PBF on 18 indicators. Due to regional heterogeneity, we evaluated the intervention sites (North and South) separately. Beginning January 2011, 11 quarters (33 months or 2.75 years) of data from 134 facilities after matching (84 in the North and 50 in the South) were used. Our econometric framework employed a multi-period, multi-group difference-in-differences model on data that was matched using propensity scoring. The regression design employed a generalized linear mixed model with both fixed and random effects, fitted using the seemingly unrelated regression technique. PBF resulted in positive impacts on MCH, PMTCT and paediatric HIV program outcomes. The majority of the 18 indicators responded to PBF (77% in the North and 66% in the South), with at least half of the indicators demonstrating a statistically significant increase in average output of more than 50% relative to baseline. Excluding pregnant women, the majority of adult HIV treatment indicators did not respond to PBF. On average, it took 18 months (six quarters) of implementation for PBF to take effect, and impact was generally sustained thereafter. Indicators were not sensitive to price, but were inversely correlated to the level of effort associated with marginal output. No negative impacts on incentivized indicators nor spill-over effects on non-incentivized indicators were observed. The PBF program in Mozambique has produced large, sustained increases in the provision of PMTCT, paediatric HIV and MCH services. Our results demonstrate that PBF is an effective strategy for driving down the HIV epidemic and advancing MCH care service delivery as compared with input financing alone.