This paper explores the process of modernisation of doctoral education and the change management approaches used in that process. The author argues that distinctive features of higher education institutions need change management approaches that are different from those used in more hierarchical organisations. A multiple case study was conducted on four public universities that went through the process of modernisation of doctoral education in four countries (Slovenia, Austria, Portugal and Montenegro). Sixteen top-level change agents were interviewed using an adapted Burke-Litwin causal model of organisational performance and change as a conceptual framework. The author presented a general framework for the conceptualisation of change management in doctoral education that considers the distributed organisation of higher education institutions and its effects on change management approaches. The research showed that the external environment, organisational culture and structure had a profound influence on the scope, goals, duration and the key features of change management methods used during the modernisation process.