In a market economy and financial crisis, the head of any medical institution has to make adequate decisions regarding the cost-effective functioning of the hospital. Along with reducing costs, the main task is to maintain a high level of medical care. In this paper, the economic efficiency of medical activities in three specialized hospitals for rehabilitation (previously called sanatoriums) in the cities of Hisar, Varna and Bankia in Bulgaria was studied. The competitiveness of the presented rehabilitation institutions lies in their ability to design, produce and offer rehabilitation services that are more attractive to patients in terms of price and quality characteristics and more fully meet their needs compared to the rehabilitation services of competitors. Based on the analysis, it was found that in rehabilitation hospitals, through long-term obligations, the purchase of short-term assets necessary for the implementation of activities is financed, and operating income is invested in long-term assets. This fact determines the increase in liabilities to the company by further minimizing free cash flows, which involve financing current activities, but are invested in non-current assets. At the same time, rehabilitation hospitals — budgetary organizations strictly comply with capital expenditures, which must be specified in the appropriate paragraph, with an approved budget according to the appropriate indicator, which proves strict compliance with budgetary discipline and control over the flow of funds.