The research objective is to formulate some suggestions for the improvement of business processes modeling in the innovative activity of the organizations for the increase in its efficiency. Having studied the existing approaches to the business processes management, theoretical works and practical experience, the authors conclude, that the standard models, developed for traditional business processes of the organizations, are insufficiently effective for the innovatively active organizations. The main objectives of modeling of business processes of innovatively active enterprise were formulated, possible tools are studied. According results of the research, some samples of business modules and subprocesses, adapted for the innovatively active organizations, are developed. The results, received by authors, can be useful for the increase in efficiency of the existing business models, as well as for the information support during the innovative projects creation and implementation. The innovatively active organizations can use the authors’ proposals to support the managerial decisions in the conditions of the need for reengineering of the operating business processes, as well as during new products launch to the market. Bodies of state regulation can use the obtained results during the formation of the innovative development strategy.