AbstractThere are several key external challenges to be mastered in the transition from the traditional university towards entrepreneurial university which are transformed into internal challenges. Unlike the business schools the management structures and environment of an university of technology may be often very cautious about implementation of the entrepreneurial elements in the technology and science study and research programmes. Often they have to be confronted by the requirements of students and businesses for more entrepreneurship education and skills in the university graduate profiles to accept this. This paper examines fundamental challenges of implementation of the concept of entrepreneurial university in two European universities of technology with direct central public funding which gradually covers less and less its future development needs. The current status of transformation towards an entrepreneurial university at the Slovak University of Technology in Bratislava compared to the University of Technology Ilmenau is described, analyzed and the next steps put forward.