The COVID-19 pandemic brought about a significant transformation in the way education is delivered, with e-learning becoming the primary mode of instruction worldwide. In the Chittagong Hill Tracts region of Bangladesh, this shift posed unique challenges for indigenous rural communities. The present study endeavours to investigate, explore, and diagnose the e-learning experience of the indigenous rural community residing in the Chittagong Hill Tracts region of Bangladesh. The research employs a qualitative approach, and three specific areas from the aforementioned region were purposively selected for data collection. In order to accomplish the research objectives, a total of 60 semi-structured, in-depth interviews and participant observations were conducted. Data analysis used both a deductive method through thematic analysis and a hybrid integrated data-driven inductive approach. The Granheim method and Nvivo-12 software were used for data analysis, processing, and coding. The result revealed that the experiences of e-learning among indigenous students of Chittagong Hill Tracts have been suffering from technical illiteracy, insufficient equipment, and devices, poor network coverage, inattention in online classes, feeling isolation, moral degradation, and online addiction. Consequently, the majority of the indigenous students had unfavourable experiences with online teaching and learning techniques. Based on the results, the study recommends strategies to provide better access to e-learning resources, improve internet connectivity, provide access to devices, and enhance digital literacy for students in remote rural areas. Furthermore, the findings of the study will be crucial for academics, policymakers, stakeholders, and development practitioners in developing a stronger e-learning policy and practice for all, particularly for the indigenous rural community in Chittagong Hill Tracts.