It is unclear whether there is any association between psychological distress and unhealthy dietary habits among adolescents in low- and middle-income countries. We aimed to estimate the prevalence of these factors in South-East Asia region and investigate their associations. We used data from the Global School-based Health Survey for nine South-East Asian countries. Psychological distress was defined by presence of ≥ 2 factors from loneliness, anxiety, suicide ideation, suicide planning and suicide attempt. We assessed inadequate fruit intake, inadequate vegetable intake, daily soft drink and weekly fast-food consumption. We used random-effects meta-analysis to estimate pooled prevalence. Logistic regressions were used to estimate OR of unhealthy dietary behaviours for psychological distress. Among 30 013 adolescents (56 % girls) aged 12–15 years, the prevalence of psychological distress was 11·0 %, with girls reporting slightly higher than boys (11·8 % v. 10·1 %). The prevalence of inadequate fruit intake, inadequate vegetable intake, daily soft drink consumption and weekly fast-food consumption was 42 %, 26 %, 40 % and 57 %, respectively. Psychological distress was associated with inadequate fruit intake (pooled OR = 1·20, 95 % CI 1·03, 1·40), inadequate vegetable intake (pooled OR = 1·17, 1·05, 1·31) and daily soft drink consumption (pooled OR = 1·14, 1·03, 1·26); but not with weekly fast-food consumption (pooled OR = 1·13, 0·96, 1·31). We observed substantial cross-country variations in prevalence and OR estimates. In conclusion, South-East Asian adolescents have significant burden of psychological distress and unhealthy dietary behaviours, with those having psychological distress are more likely to have unhealthy dietary behaviours. Our findings will guide preventative interventions and inform relevant policies around adolescent nutrition in the region.