Digital Transformation (DT) has become the core motivator for almost all organizations worldwide. In order to cope up with the new demands, Higher Education Institutions (HEIs) are also giving due consideration to digitizing their services, including pedagogical services. Many challenges are being faced during the successful adoption of DT strategies and plans. One of the main obstacles is the set of challenges related to the stakeholders in HEIs; more precisely, instructors and students. This paper extracts, synthesizes, categorizes, and prioritizes the challenges hindering the success of DT in Saudi universities. Firstly, the paper extracts the main challenges faced by instructors and students, and then constructs a model of the challenges based on the tripartite classification of attitude. The paper adopts a Multi-Criteria Decision Making (MCDM) Method, called the Analytic Network Process (ANP), for the purpose of gathering instructors’ and students’ evaluations and prioritizing their challenges accordingly. A total of 25 instructors and students were recruited from various HEIs in Saudi Arabia to evaluate the model. The results show that learning performance, lack of access to resources, and fear of change are the most significant factors hindering students towards successful adoption of DT. On the other hand, fear of change followed by lack of experience and privacy concerns are the most significant factors hindering instructors towards successful adoption of DT. The research is intended to enlighten decision-makers in Saudi HEIs to consider non-technical challenges while planning for digitizing HEIs services.