The purpose of the article is to develop the model to optimize the process of managerial decision-making for the innovation and investment activities of pharmacy networks, especially in conditions of their financial self-development. It was shown that the current state of the pharmacy business is characterized by the active development of pharmacy retail. Analysis, which based on the information of the syndicated database “Axioma” during 2015-2017 years, showed, that number of pharmacies increased up from 15262 to 16192 units. The most significant regions of Ukraine in terms of the pharmacies number are Kiev, Dnipropetrovsk, Odessa, Kharkiv and Lviv regions. A clearly expressed trend in the development of modern pharmacy networks is their consolidation, which is directly related to the activation of their investment activities. This raises the need to develop and implement a model that optimizes the in innovation-investment process. In this model, it was proposed to include three interrelated and interdependent blocks: a block for the formation of an optimal innovation-investment portfolio, a block for selecting an innovation-investment project, and a block for calculating project’s cash flows. The article describes each of the blocks and the sequence of execution each of the stages. In order to optimize the innovation-investment projects’ portfolio, the objective function of maximizing the portfolio’s net present value was proposed. This function considers financial constraints on the possibility of attracting resources for the project’s implementation. For the primary selection of innovation-investment projects, the use of the benefit-cost criterion was justified and the formula for its calculation was presented, taking into account the peculiarities of the pharmacy networks. The use of the model proposed by the authors will help to reduce the likelihood of errors in making management decisions, and, consequently, increase the efficiency of innovation and investment processes and sustainable financial self-development of pharmacy network.