Massive open online courses (MOOCs) are among the latest e-learning initiative that have gained a wide popularity among many universities. Student dropout in MOOCs is a major concern in the higher education and policy-making communities. Most student dropout is caused by factors outside the institution’s control. In this study, a multiple-criteria decision-making method was used to identify the core factors and possible causal relationships responsible for the high dropout rate in MOOCs. Twelve factors, distributed across four dimensions, related to students’ dropout from online courses were identified from the literature. Then, a total of 17 experienced instructors in MOOCs from different higher education institutions were invited to assess the level of influence of these factors on each other. The results identified six core factors that directly influenced student dropout in MOOCs, these were: academic skills and abilities, prior experience, course design, feedback, social presence, and social support. Other factors such as interaction, course difficulty and time, commitment, motivation, and family/work circumstances were found to play a secondary role in relation to student dropout in MOOCs. The causal relationships between the primary and secondary factors were mapped and described. Outcomes from this study can offer the necessary insights for educators and decision makers to understand the cause–effect relationships between the factors influencing MOOC student dropout, thus providing relevant interventions in order to reduce the high dropout rate.