The aim of the study was to assess the prevalence of fruits and vegetable consumption and associated factors among Southeast Asian in-school adolescents. Data were collected by self-report questionnaire from nationally representative samples (total 16,084) of school children aged 13 to 15 years in five Southeast Asian countries. Overall, 76.3% of the 13 to 15 year-olds had inadequate fruits and vegetables consumptions (less than five servings per day); 28% reported consuming fruits less than once per day and 13.8% indicated consuming vegetables less than once per day. In multivariable analysis, lack of protective factors and being physically inactive were associated with inadequate fruits and vegetable consumption, and sedentary behaviour and being overweight was protective of inadequate fruits and vegetable consumption. The results stress the need for intervention programmes aimed at increased consumption of fruits and vegetables, targeting proximal factors such as the family environment and distal factors by aiming at integrating other risk factors such as physical activity into health promotion among adolescents.