Graduate education system is in the process of ongoing changes driven by the employers’ requirements, ongoing demographic changes, changes in students’ career expectations and the new vision of a wider scientific enterprise. There is a need to refocus graduate educational system from the needs of the academic institution and related research towards student-centered paradigm. The purpose of this research is to analyze the practice of STEM doctoral studies from the student-centered perspective by examining a case practice from a doctoral educational event. The paper deals with the questions whether the aims and expectations of graduate students are consistent with the goals and requirements of academics (researchers and teaching staff of higher education) and to what extent; what aspects of academic policy and pedagogical approaches correspond to the needs and requirements of the non-academic and innovative industries; and how the students understand their career prospects in terms of innovation, future job requirements, and knowledge-based entrepreneurship requests. In order to address this problem, a case study was conducted in four dimensions: academia, pedagogy, industry and entrepreneurship. As a result, a qualitative study provided several implications for organizations preparing future researchers and employees. The results show which students’ needs, challenges and problems and relevant requirements for academic institutions are related to the prospects of STEM education with an emphasis on computing (computer science) and software engineering as an integrating part.