This paper explores and assesses the presence/absence of institutional arrangements in educational settings for addressing the concerns of gender-variant children (GVC) through a sample survey of schools in the three-country context of India, Sri Lanka and Nepal. This research highlights the need for effective regulatory, normative and cognitive structures to address issues of childhood gender variance. With a contextual analysis of recent developments and comprehensive study of data reports in the three countries, the study analyses multiple dimensions of discrimination and bullying of GVC in educational settings. Using qualitative and quantitative methods, this paper highlights causes and issues associated with the problems of GVC as well as affirmative actions and institutional practices required to be implemented in schools in the three-country context. The results and findings provide evidence that academic institutions in India, Sri Lanka and, to some extent, Nepal lack institutional mechanisms to address issues of homophobia, abuse by peer group, mental health issues, emotional challenges, social discrimination, lack of opportunities, lack of monitoring and counselling, micro-level engagements and high dropouts of GVC. This study also charts out futuristic agenda, such as comprehensive mapping of GVC in schools, implementation of effective counselling mechanism, the need to create and adopt basic reference module for educators around gender diversity and variance.