Relevance of the chosen subject of research is caused by the fact that the development of innovative market economy requires a more flexible reaction of the education system and its mobility. Combining the training process with the operating activities of a production enterprise is necessary, and the subjects of the infrastructure of the regional knowledge market are therefore required to complement the state system of bachelor training by personnel training aimed at specific jobs at the production enterprises of the region. The purpose of the study is in developing an approach for evaluating the competences of university graduates on the regional knowledge market, and developing instruments of innovative management providing profitability and financial independence of public educational institutions on this basis. In accordance with the purpose of the study, the following tasks are solved: analysis of the performance of the Vologda State University and similar institutions by the method of operating cycle, development of the innovative project helping to achieve the optimal criteria of the operating cycle, efficiency evaluation of the "Innovations" bachelor training program. The performance parameters of the universities were analyzed by the method of operating cycle. We have revealed the need to develop an innovative project aimed at achieving the optimal criteria of the operating cycle. We have offered an approach for organizing educational activities as a continuous process of developing innovative projects. We have paid special attention to investors that are the entities of the engineering business and the subjects of the regional knowledge market. It is proposed to use a monetary equivalent of the cost of gained knowledge as the economic result from investing into educational programs. As the performance of professionals depends on the level of their competence and the amount of gained knowledge, a conclusion can be drawn on the correlation between the size of the compensation and the knowledge gained by a graduate during the training process. The performed evaluation has shown that on average, the cost of knowledge of the VoSU graduates is estimated by employers at 15 322 rub., or 2.5 minimum wage rates per month. In 4 years the return from the knowledge constitutes 735 456 rub., which is 2.26 times more than the investments (costs) for obtaining this knowledge. A possible application of the study is using its results for increasing the profitability and financial independence of higher education institutions.