Excessive body weight during adolescence represents a significant public health problem worldwide. Identifying factors associated with its development is crucial. We estimated the prevalence of overweight and obesity in a representative sample of 11, 13 and, 15-year-olds living in Greece and explored the association with diet-related behaviours and habits. Self-reported data on weight, height, diet-related behaviours and habits were used from 3816 students (1898 boys, 1918 girls) participants in the Greek arm of the international Health Behaviour in School-Aged Children (HBSC) study during 2018. Overweight and obesity were defined using the 2007 WHO growth charts classification. Prevalence of overweight was 19.4% in the total sample, 24.1% for boys and 14.7% for girls, and prevalence of obesity was 5.3% in the total sample, 7.3% for boys and 3.4% for girls, respectively. In the total sample, overweight (including obesity) was positively associated with male gender, low family affluence, skipping breakfast, and being on a diet, and inversely associated with age and being physically active. Eating rarely with the family was positively associated with overweight only among boys and eating snacks/meals in front of screens only among girls. No association was noted for eating in fast-food restaurants, consuming vegetables, fruits, sweets, and sugar-sweetened beverages.