This chapter has developed a methodological approach to the evaluation of indicators of the economic efficiency of medical institutions related to systems that are difficult to formalise, both according to a variety of indicators that evaluate the activities of these institutions by medical type: outpatient care, availability of inpatient care to the population, indicators of preventive work and economic aspects. However, all these indicators are scattered and are not brought together in a general criterion of effectiveness that could be predicted when planning the “health” section of the regional or municipal budget and, moreover, for the optimal management of medical institutions on the basis of the criteria listed above. The chapter develops the idea of computer technology for the preliminary assessment of the financial and economic activities of medical institutions, proposed on the basis of artificial intelligence using neural network modelling. The proposed provisions were tested in computer experiments on real data and proposals were made for the generalised management of the economic results of medical institutions. The results of the study show that the use of neural network modelling creates the basis for increasing the reliability and objectivity in the assessment of the economic activities of medical institutions and for improving the effectiveness and quality of medical services.