The concept of inclusive education is an old one, but the implementation of this concept in practice is still connected with realms of difficulty, especially in South-Asian countries like Bangladesh. Although Bangladesh is a multilingual country with multiple ethnicities, few of its educational systems are concerned greatly with inclusion, e.g., of children with special needs in schools, much less with more comprehensive notions of inclusion. Added to this, the inclusion of indigenous children in mainstream education is a major challenge in the present situation. The recently launched educational programme for teaching multilingual education (MLE) based on a culture’s originary language or ‘mother tongue’ (MTB) could assure greater inclusion of indigenous children as an effective practice in Bangladeshi education. The authors report a study regarding implementation of the programme in the Chittagong Hill Tracts. The objective of the study was to identify obstacles and develop methods to improve mother tongue-based skills for early stages of primary education among indigenous children in that region. The authors found that some essential practices need to be activated with specific objectives for actual advancement of the inclusive education within the programme. Impediments to the implementation and development of the programme were studied and evaluated. The study found that development of modified, more inclusive material for learners, enthusiastic training for educators and infrastructural support for educational institutions in practical ways were all beneficial. The research was planned and conducted in three phases based on a qualitative multi-method approach. The study explored the perception and practice of indigenous education by teachers and parents in three school districts of the Chittagong Hill Tracts. The ideas, views and experiences of the stakeholders were also analysed in order to identify how to improve the existing condition of indigenous education. Finally, it is argue that, by embracing its positive developments as a priority, the MTB-MLE programme could become an essential tool for inclusive education.