Purpose The purpose of this paper was to evaluate the efficiency of secondary education schools in Chile. Since the early 1980s, several educational reforms have been passed with the main objective of improving the quality, equity and efficiency of the Chilean education system. This has initiated a debate about the efficient use of public educational resources. In response, this study provides insights into identifying the most efficient types of schools based on a set of different inputs and outputs. Design/methodology/approach This quantitative research study used data envelopment analysis (DEA), which estimates a single index of efficiency to identify schools performing at superior levels compared to other schools with similar characteristics. Two sets of models are created for evaluating efficiency. The first set of analyses provides a longitudinal efficiency comparison based on student performance on two national standardized tests as outputs, and the second model incorporates socioeconomic characteristics of students attending different schools as inputs in the efficiency estimation. Findings Based on the longitudinal models, it was found that private schools are more efficient and more consistent in maintaining their efficiency over time than other types of schools. In addition, when accounting for socioeconomic factors, publicly subsidized schools were more efficient than public schools. Practical implications The Chilean parliament is currently discussing new educational reforms that focus on more efficient use of educational resources to improve educational quality and equity. The results provided in this study generate useful evidence for policymakers and other stakeholders regarding school efficiency and the appropriate allocation of public resources to support diverse students served by different types of secondary educational institutions. Social implications Education is a key factor affecting social mobility and socioeconomic improvement of societies. Schools are called upon to improve their performance to promote these social goals. Accordingly, more novel forms of research on efficiency are necessary to assess how well schools are transforming their inputs into performance outputs. Originality/value This study provides a longitudinal analysis of educational efficiency using DEA with a national data set of Chilean schools to evaluate how consistent the schools are in maintaining their levels of efficiency over time. In addition, one DEA model accounts for a social “vulnerability” index at the student level to better understand how efficiently secondary schools use their resources. The insights gained provide data-driven answers to support more informed educational decision-making and policy processes in Chile.