The physical and social challenges associated with neuromuscular disorders may impact mental wellbeing in non-ambulant youth during the more vulnerable period of adolescence. This cross-sectional survey investigated non-ambulant youths’ mental wellbeing and relationships with physical health, participation and social factors. The conceptual model was the International Classification of Functioning, Disability and Health (ICF). Thirty-seven youth aged 13–22 years old (mean age 17.4 years; n = 30 male; n = 24 Duchenne Muscular Dystrophy) and their parents provided biopsychosocial data through a comprehensive self-report questionnaire. The primary outcome measure was the Warwick Edinburgh Mental Wellbeing Scale (WEMWBS). Relationships between mental wellbeing and variables within and across each ICF domain were explored using linear regression models. Mean WEMWBS scores (55.3/70 [SD 8.1]) were higher than for typically developing youth and comparable to youth with other chronic conditions. Over half of youth reported severe co-morbidities across all body systems. Multivariable modelling indicated that mental wellbeing was independently associated with academic achievement and perceived family support but not with physical health variables. Beyond management of physical co-morbidities, enabling youths’ educational attainment and attending to social support likely optimises youth's wellbeing.