Objective: We aimed to determine the prevalence and factors associated with loneliness among adolescent students in three South Asian countries.Methods: We used data from the latest Global School-Based Health Survey of Afghanistan, Bangladesh, and Pakistan. A two-stage cluster sampling design was used to collect the cross-sectional survey data. Data from 8 089 in-school adolescents were analysed using STATA 14.0.Results: Among all the participants, the prevalence of loneliness was 14.9%. The prevalence of loneliness was significantly higher in females (19.7%), Afghan adolescents (35.5%), participants having anxiety-induced sleep disturbance (51.4%), often experiencing bullying (28.9%), feeling hungry often or always (23.9%), suffering parental emotional neglect (21.2%), and spending >= 8 hours/day leisure time (35.8%), than their counterparts. The final adjusted model of multiple logistic regression showed that females (OR = 1.36, 95% CI: 1.02 -1.80), having no close friends (OR = 2.00, 95% CI: 1.30 - 3.10), having an anxiety-induced sleep disturbance (OR = 5.25, 95% CI: 3.75 - 7.34), being bullied 1 to 2 days in the past month (OR = 2.13, 95% CI: 1.60 - 2.84), being physically attacked 2 or more times in the past year (OR = 1.69, 95% CI: 1.26 - 2.26), suffering parental emotional neglect (OR = 1.67, 95% CI: 1.18-2.34), and current tobacco user (OR = 2.70, 95% CI: 1.39 - 5.25) had significantly higher odds of having loneliness.Conclusion: We found a higher prevalence of loneliness and identified several risk factors among in-school adolescents in three South Asian countries. To reduce loneliness among in-school adolescents, target-oriented interventions, such as peer, parental, and counselling support, are needed at schools.