Purpose This study aims to identify the efficiency scores of hospitals affiliated to the Ministry of Health in Turkey between the years of 2010-2015 at provincial level and to reveal the factors that affect the efficiency scores. Design/methodology/approach The two-stage data envelopment analysis (DEA) method was used to achieve the study purpose. In the first stage, DEA method based on input-oriented Charnes-Cooper-Rhodes (CCR) model was performed to calculate the efficiency scores of public hospitals at the provincial level between 2010 and 2015, and in the second stage, Tobit regression and linear regression analyses were used to identify whether the efficiency scores of provinces are affected by the input, output and control variables. Findings Upon the analysis, the average efficiency scores of 81 provinces by years were found to vary between 0.79 and 0.89. According to both regression analyses, all of the input and output variables were found to have significant effects on the efficiency scores of provinces while only the population of province among the control variables was identified as the factor with an effect on the efficiency scores of provinces (p < 0.05). Practical implications The results of this study are thought to guide health policymakers and managers in terms of both determining efficient and inefficient hospitals at the provincial level and revealing which variables should be taken into account in order to increase efficiency. Originality/value The study differs from previous studies on the efficiency of hospitals. First, although previous studies were generally descriptive studies to determine the efficiency level of hospitals, this study is an analytical study that tries also to show the factors affecting the efficiency of hospitals. In addition, while examining the effect of input and output variables on efficiency scores, control variables were also included in the study.