Numerous factors, including inefficient utilization of healthcare resources have been attributed to the poor health outcome. The study aims to compare the efficiency of health expenses and its determining factors in the emerging economies based on their income levels. Data for the study is extracted from the World Bank’s World Development Indicators for 21 countries covering the period of 2000 to 2018. Analysis of the research involves two stages. Stage one computes the efficiency scores, whereas second stage examines factors affecting health efficiency by employing the Tobit regression and Simar-Wilson regression test to confirm the results. The Tobit result shows that research and development (R&D) and physicians enhanced health efficiency at the main panel, lower-middle-income, upper-middle-income, and high-income countries. Corruption remained negative with education showing mixed results. The interaction between research and development and physicians increases health efficiency in all the panels. Health research must be a policy focus if efficiency is to be achieved by the emerging economies.