Currently, assessing the effectiveness of financing government program is a topical issue in theory and practice, since the level of health care development is directly related to the level of socio-economic development of the region. The goal of the research is development of methodological tools for efficiency assessment of the implementation of government program in the health sector, focused on quality improvement of life of the population. The methodological basis of the research is general scientific methods of comparison, analysis, synthesis, tabular representation of data. The methodological toolkit has been tested using official data from the Federal State Statistics Service of the Russian Federation, the Ministry of Finance of the Russian Federation for 2018-2019. The result of the work is development of distribution matrix of Russia’s regions for certain segments. The aim of the distribution is ranking regions and makes it possible to identify subjects with a high, medium and low level of effectiveness of program implementation.