This qualitative study explored Bhutanese parents’ perceptions of the benefits and their concerns in relation to the inclusive education of their children with special educational needs (SEN). Twenty-six parents (13 fathers and 13 mothers) of children with SEN, either fully or partially included in three pilot schools with SEN programmes located in urban, semi-urban, and rural regions in Bhutan were individually interviewed. The thematic analysis of the interview transcripts revealed that inclusion was associated with social benefits for parents of children with developmental disabilities, while parents of children with physical disabilities perceived the caring and supportive environment as the major gain from inclusion. For a few parents, the inclusion of their child in the school alleviated some of the burden of daily care. Most parents were satisfied with their children in the school, despite limited school resources, although their concerns for behavioural problems, bullying and lack of academic learning persisted. Implications for parent advocacy in the school and the need for counselling both for parents and their children, and training for teachers are discussed.