ABSTRACT Backgrounds Research concerning student-centered learning (SCL) recommends a comprehensive assessment of medical students’ competencies including their personal and professional characters. Accordingly, nurturing future doctors should be in a continuous mentorship program. However, in a hierarchical culture, communication is one-way with limited feedback and reflection. We aimed to explore challenges and opportunities for SCL implementation in medical schools in this cultural setting necessary for a globally interdependent world. Methods Two cycles of participatory action research (PAR) were conducted, involving medical students and teachers in Indonesia. A national conference on SCL principles was conducted between the cycles, also the SCL modules were developed for each institution and feedback was shared. Twelve focus group discussions were conducted (before and after the module development), with 37 medical teachers and 48 medical students from 7 faculties of medicine across Indonesia at various levels accreditation. Following verbatim transcriptions, a thematic analysis was conducted. Results and Discussions In cycle 1 PAR, some challenges in implementing SCL were identified: lack of constructive feedback, overloaded content, summative-based assessment, hierarchical culture environment, and teachers’ dilemma of committed time between patient-care and education. In cycle 2, several opportunities to approach the SCL were proposed: a faculty development program on mentorship, students’ reflection guides and training, a more longitudinal assessment system, also a more supportive government policy on the human resources system. Conclusions The main challenge of fostering student-centered learning revealed in this study was a teacher-centered learning tendency in the medical curriculum. The weighting towards summative assessment and the national educational policy drive the curriculum like a ‘domino effect’, away from the expected student-centered learning principles. However, using a participative method, students and teachers could identify opportunities and articulate their educational needs, i.e., a partnership-mentorship program, as a significant step toward student-centered learning in this cultural context.