The advent of computer technology and widespread use of internet has given rise to e-learning and blended programs all over the world. The aim of this study was to explore problems faced by students enrolled in blended program of MHPE in Pakistan.This was a qualitative exploratory study done between October 2017 and February 2018. Data included semi-structured individual interviews of eighteen students and four facilitators involved in blended MHPE programs of three leading Universities of Pakistan. Nine hundred and two students' reflective essays were also included for data triangulation. Data was organized in Atlas-ti and analyzed through thematic analysis using Revised Community of Inquiry framework.Seventy open codes were condensed to fifteen sub-themes and five themes. Learner related problems comprised difficulty in self-regulation and self-directed learning as emphasized by the facilitators whereas students quoted teacher related problems focusing on feedback provision. Cognitive issues included huge cognitive load with engagement issues. Students also highlighted issues with social interaction encompassed difficulties in interacting with facilitators and managing group dynamics. Both students and facilitators agreed on institutional issues focused on limited resource provision, unsatisfactory administrative support and financial issues.Students of MHPE are challenged with variety of issues in blended learning program relating to self-regulation, heavy cognitive load with engagement, social interaction especially with facilitators and managing group dynamics Addressing these issues can improve the experience of these students in blended programs.