The article analyzes the current state of innovation activity of small enterprises. Based on the statistical data there are presented such parameters as the proportion of small enterprises engaged in innovative activities, proportion of innovative goods and services of small enterprises, cost of the innovation activities of small enterprises. There has been mentioned the importance of the assessment of innovative activity as a means of timely identification of problems and building solutions to improve the activity of the innovative enterprises in the science city and to increase their efficiency. As a result of the analysis, the main components of innovation activity in the science cities needed for the objective assessment have been identified. The proposed assessment is based on the principles of consistency, systematicity, complexity, practical orientation, scientific character, optimality, democracy, and reliability. In accordance with the developed principles, there has been described the proposed approach to assessing the innovation activity in the science cities. The requirements for developing assessment parameters are identified and its methodological provisions are formulated, where the goal, objectives, principles, the process of assessing, etc. are stated in a logical sequence. The sequence of the process includes forming the staff responsible for the assessment, calculating indicators, interpretation of the results. The coefficients, such as the level of added value, the profitability of intangible assets, the assessment of investments in the implementation and development of R&D, the volume of commercialized R&D have been proposed to take into account as assessment parameters. On the basis of small innovative enterprises of the science city of Korolev SPE Inkar-M LLC, SPE Impulse LLC, Robotmash LLC there has been carried out the approbation of the assessment, the results of which gave the highest rates of their innovative activity.