BACKGROUND Adolescence is considered a nutritionally vulnerable period of life, since their eating habits are influenced by factors that can promote the consumption of non-nutritious food. OBJECTIVE To analyze the relation between eating habits, obesity, and the perception of Health-Related Quality of Life in school-aged adolescents. METHODS A cross-sectional study of 550 adolescents aged 16 ± 1 years (60% women) attending a public education institution in Valparaíso, Chile. The Global School-based Student Health Survey (GSHS) for eating habits and the KIDSCREEN-27 survey for health-related quality of life were self-administered online. The answers were anonymous. A logistic regression analysis was conducted to evaluate the relationship between the variables, which was adjusted for age and sex. RESULTS Ten percent of men and 6% of women were obese. Those with an inadequate consumption of fruits had a worst perception of their physical well-being, autonomy and relationship with their parents. Psychological well-being and school environment were perceived worst among those that did not consume breakfast. Obese respondents also reported a poorest physical health. CONCLUSIONS Inadequate eating habits and obesity have a negative effect of health-related quality of life among adolescents.