Labour migration from Nepal has contributed significantly to the nation’s wealth, yet it has negatively affected the health and well-being of migrant workers. Until recently, limited research into the impact of parental migration on left-behind adolescents existed in Nepal. This study therefore aims to address this gap by conducting a cross-sectional study in Nawalparasi, one of the highest migrant-workers-sending districts in Nepal, involving 370 left-behind adolescents and 388 non-left-behind adolescents. Psychosocial well-being was measured using the Nepali version of Youth Paediatric Symptom Checklist (Y-PSC) and Strengths and Difficulties Questionnaire (SDQ). The survey was conducted in schools, and the overall response rate was 95.83 per cent. Most participants were in grade 10 (53.6%), with over half being female (51.2%) and a mean family size of 4.73 ± 1.52. Among them, 17 per cent experienced psychological problems, with left-behind adolescents showing a higher prevalence of low psychological well-being (20%) and psychological dysfunction (21%) compared to non-left-behind adolescents (13% and 14%, respectively). Adolescent females exhibited higher rates of psychological problems (21% vs. 12%) and dysfunctions (21% vs. 13%) than males in both groups. Perceived relationships with parents were strongly linked to psychosocial health, with left-behind adolescents being more likely to experience psychological issues and dysfunction compared to non-left-behind adolescents. Similarly, factors such as communication with migrated parents, visit intervals, social media use, and mobile access were associated with the psychosocial health of left-behind adolescents. The finding suggests that adolescents with migrant parents experienced poorer psychosocial well-being, suggesting that school-based mental health programs could help support their well-being.