Rapid development of using information technology in higher education contributes not only into its efficiency but also may cause a variety of risks affecting implementation of some other educational process aspects. Understanding the significance of the risks and their subsequent study and assessment allows for timely adjustments in implementation of certain informational and educational technologies in the educational process. The paper focuses on the issues related to identification of the major risks while introducing and implementing educational innovations, and those related to introduction of the learning management system (LMS) in higher education institutions, their impact assessment and influence on the efficiency throughout the entire educational process. The results of the study have been summarized using risk mapping and sensitivity analysis methods. These methods allowed us to visualize the level of each risk distinguished in the study according to the degree of its influence on the educational process and probability of its occurrence. The study was based on the survey findings and students’ interviews and aimed to identify whether they understand and realize the difficulties and complexities in the procedure of innovative technologies implementation by their university. The authors have developed a list of risks occurring while introducing and implementing innovations in the educational process which in their turn will reflect the peculiarities of the higher education institution using modern learning techniques. Moreover, the paper discusses the risk sensitivity study results. They are presented as an expert appraisal of risks related to their influence on the resultant as integrated assessment, i.e. the Wheel Model of risk management. In the course of the study it has been found that, despite the difficulties of innovation implementation, the innovative programs having been introduced improve the educational process and ensure appropriate quality of human capital, or workforce. Reasonable conclusions from the experience of the state-of the art innovation introduction into university teaching-learning process confirm its practical significance, its ability to encourage university students and increase their participation and independence in learning, thus contributing to development of their skills that meet the requirements of an economist position and in future will help them be successfully engaged into innovation economics. These students’ skills and competencies meet the requirements of innovative processes in the economy, despite the fact that the process involves certain risks. The paper materials may be of practical value to professionals involved in the development and implementation of innovative educational technologies at universities.