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Since the early 2010s, Mongolia has been reinforcing its universal health coverage. However, with the economic crisis of 2012, the country has been faced with severe constraints that drastically limit the possibility of increasing the public financing of health expenditure in a sustainable way. In this context, improving the efficiency of health facilities, particularly primary health facilities, which plays a fundamental role in universal coverage, is of key importance. In this paper, we analyze the efficiency of Soum Health Centers, which provide the bulk of primary care in rural areas, as well as a selection of factors associated with their performance. We collected data on the activity and resources used in all health centers in five rural regions of Mongolia between 2013 and 2015. We apply a double bootstrap DEA procedure to calculate unbiased efficiency scores and to estimate the effects of potential determinants. The centers in our sample have a low overall level of efficiency, indicating that they could significantly increase their provision of healthcare services with the same quantity of inputs. The results highlight the important role of factors related to the demand for care in explaining the differences in efficiency. More broadly, they show the value of strengthening the efficiency of healthcare facilities in a context of significant macroeconomic constraints.