The objective of this paper is to explore the learning challenges of a group of first-year Papuan medical students. Perspectives were obtained from a group of Papuan medical students (attaining high and low grades) and Faculty staff (Papuan and Non-Papuan) at the University of Cenderawasih, Indonesia. This qualitative case study research employed semi-structured interviews conducted online via Skype. Data were analysed using a general inductive method and classified into themes to reflect Papuan students' learning challenges. We identified three main themes, namely the "individual," the "university" and the "outside environment." We found that these Papuan students were affected by their individual challenges, such as self-perception and the level of their learning and social skills. At the university level, students faced difficulties in adjusting their learning and felt that they were lacking a quiet supportive learning environment. They were also influenced by outside environment factors, such as family and financial concern. Given the wide range of challenges faced by Papuan medical students, Faculty development initiatives incorporating cultural responsiveness into the curriculum and wider government support are crucial for the successful educational advancement of Papuan medical students, which ultimately leads to better health outcomes for the Indigenous people of Papua.