This paper measured the variations in performance of small municipalities in the State of São Paulo, Brazil, regarding the technical efficiency in the use of public funds in public primary health care actions concerning the funding profile, in a scenario of fiscal federalism. Technical efficiency is one of the parameters of evaluation of public sector performance and was measured by means of Data Envelopment Analysis (DEA). The correlation analysis of DEA score was used to verify possible associations between technical efficiency and the funding profile of expenses with health care. The results showed that 6.41% of the municipalities were considered efficient. They also showed that the level of municipality dependence to inter-governmental general purpose grants and the national health funding specific purpose grants have negative correlation with efficiency scores.