This paper aimed at establishing the treatment of gender-nonconforming learners in Namibian schools. The provision of education in Namibia is based on the principles of non-discrimination and equal access to quality education for all as stipulated in the Namibian constitution. Even though there is growing evidence on the mistreatment of gender-nonconforming learners in schools world wide, there is a paucity of literature on the treatment of gender-nonconforming learners in the Namibian education context. This paper employed a case study design as a transformative research method informed by the social identity perspective. One hundred and eighty-two teachers were randomly sampled into the study, and one deputy Director of Special Programs and Schools, one deputy Director of Diagnostic, Assessment and Training Services, one regional school counsellor and one inclusive education officer at the National Institute for Educational Development were purposively sampled. The findings revealed that societal, religious, and cultural beliefs in schools were determinants of how gender-nonconforming learners were treated in some schools. A supplementary framework for the implementation of inclusive education policy (SFIIEP) was developed from the findings of this study. It is recommended that the Ministry of Education, Arts and Culture align the SFIIEP to the inclusive education policy implementation to enable open discussion of sex education topics during life skills lessons, creation of supportive learning environments, and establishment of anti-bullying policies with specific measures on curbing homophobic bullying as well as strengthening the psychological support to learners.