The health system in many parts of Nigeria has been dysfunctional in several domains including financing, human resources, infrastructure, health management information system and hospital services. In an attempt to scale up Maternal and Child Health (MCH) services and ensure efficiency, Ebonyi State Government in Southeast Nigeria provided funding to mission hospitals across the State as a grant. This study used nonparametric method to assess the effect of this public financing on the efficiency of the mission hospitals. Operational cost and number of hospital beds were used as the input variables, while antenatal registrations, number of immunization doses and hospital deliveries were the output variables. The hospitals were disaggregated into 15 hospital-years. The mean overall technical efficiency of the mission hospitals was 84.05 22.45%. The mean pure technical efficiency was 95.56±6.9% and the scale efficiency was 88.05±22.20%. About 46.67% of all the hospital-years were technically and scale efficient. Although, 55.33% were generally inefficient, only 33.33% of hospital-years exhibited pure technical inefficiency. Low immunization coverage was the major cause of inefficiency. The study showed increased maternal health service output as result of public funding or intervention; however, the mission hospitals could have saved 16% of input resources if they had performed efficiently. It also shows that data envelopment analysis can be used in setting targets/benchmarks for relatively inefficient health facilities, and in monitoring impact of interventions on efficiency of hospitals over-time.