Adolescents are an at-risk group for circadian misalignment. The contribution of sleep–wake rhythm instability to the psychoemotional, cognitive, and weight disorders of adolescents has been studied in sufficient detail. At the same time, there is insufficient information about the association between chrononutrition indices and the well-being of adolescents. The aim of this study is to investigate the relationship between chrononutrition indices and academic achievement, psychoemotional state, and anthropometric indicators in adolescents. The study involved 12,759 students in grades 6–11 of secondary schools, aged 14.2 ± 1.7 years old; 57.2% of whom were girls. Participants provided personal data, frequency and time of meals during the day and at night, on weekdays and weekends, and completed the Zung Self-Rating Depression Scale and the Yale Food Addiction Scale. There is a U-shaped association between eating mid-phase (EPFc), eating jetlag (EJL), and eating window (EW) with GPA, ZSDSI, and FA. At the same time, the frequency of night eating (NE) is linearly associated with the studied parameters. NE is the strongest predictor of ZSDSI (β = 0.24), FA (β = 0.04), and GPA (β = −0.22). EPFc, EJL, and EW practically do not differ in the strength of their association with the studied indicators. ZSDSI is most closely associated with the chrononutrition indices. There is a weak negative association between BMI and EW (β = −0.03) and NE (β = −0.04). Thus, circadian eating disorders are more often observed in adolescents with poor academic performance, high levels of depression, and food addiction.