The spread of medical technologies underpins the transition to the next global economic mode and requires large-scale investments in health sector. To substantiate them, certain methods of making investment decisions which corresponds to a new stage of scientific and technological development are required. This paper proposes the methods of investment projects evaluation based on the cost and benefit analysis, that measures both costs and benefits in monetary terms, taking into account these approaches. On the one hand, economic (public) efficiency is determined with the social effects along with other public effects being highlighted. On the other hand, financial (commercial) efficiency is calculated with a detailed presentation of investment in working capital and terminal value. In applied project analysis, working capital is either not taken into account, or simplified methods are preferred. The paper focuses on the issues of modeling investments in the growth of net working capital. A comparative analysis of working capital modeling methods in the financial models of various international organizations (UNIDO, World Bank, Asian Development Bank) and official Russian methods is carried out. Also, the author's modified method for calculating investments in working capital based on separate financial turnover and liquidity ratios is proposed, which allows taking into account industry specifics of health projects. The system of the proposed methods was tested on the example of a real project of the construction of seven urban outpatient hospitals in Novosibirsk. The results of the financial analysis with three options of working capital accounting and the economic analysis with the presentation of social, tax and redistributive effects of working capital clearly show the impact of assessing working capital requirement on the results of not only financial, but also economic efficiency, including the efficiency of participation in the project. In the frame of the economic analysis, substantial social effects for patients of new outpatient hospitals and other residents of the Novosibirsk Region were highlighted, while in the frame of financial analysis, significant effects of working capital and terminal cost for direct project participants were identified.