Background Payment mechanisms for health care providers have been used as a strategy to improve management, health indicators, cost containment, equity and efficiency. Among the mechanisms implemented in the past decade is pay-for-performance (P4P). In Chile, it was incorporated since 2003 in primary care in addition to the salary by seniority and training. Objectives To assess the impact of P4P on the efficiency of primary oral health care providers in Chile. Methods We performed a retrospective cohort study to compare the performance of oral healthcare practices belonging to primary health providers measured by the rate of dental discharge in 6 year-old children between years in which P4P was used and years in which P4P was not used, in the 52 municipalities of the Metropolitan Region of Chile. We also explored whether rurality, and the human development index (HDI) had an association with the efficiency of health care teams. We calculated the rate of discharge per 1000 patients, and its adjusted and unadjusted association with the predictors of interest, using a Random-effects Poisson regression. Results We found statistically significant differences in the rate of dental discharges when comparing P4P versus no P4P (822.59/1000 and 662.59/1000, respectively, p < 0.0001) and high versus low HDI (692.23/1000 and 832.85/1000, respectively, p = 0.01). Rurality was not statistically associated with P4P (727.24/1000 in rural and 770.19/1000 in urban municipalities, p = 0.553). Unadjusted and adjusted rate ratios were very similar. Conclusions P4P financial incentives can improve the performance of primary care dental practices, and seem to be useful interventions to improve the performance of oral health care providers.