The objective of this paper is to develop a practical E-learning framework with implementation of case method and project-based learning. In paper we obtain the following results. Content of the massive open online course (MOOC) “Safety and Security of Control Systems” is analyzed. This MOOC was introduced in 2017 for master students program “Cybersecurity” at National Aerospace Uni-versity “KhAI” (Kharkiv, Ukraine). A core part of this MOOC is a project devot-ed to safety and security assessment of real systems and software. Taxonomy for indicators of E-learning effectiveness is proposed. Case study was done in Ukraine between students of Cybersecurity program after finish of study of the MOOC “Safety and Security of Control Systems”. A sample includes 40 master students involved in the course learning during 2017-2019. Case study results confirmed a set of hypotheses related with E-learning effectiveness when case method and project-based learning are implemented.