Background: Evidence assessing the relationship between chronotype and disordered eating in adolescents is scarce. The current study tried to evaluate the association between chronotype and disordered eating in a sample of Spanish adolescents. Methods: This secondary cross-sectional study analyzed data from the Eating Healthy and Daily Life Activities (EHDLA) study. The sample consisted of 703 adolescents (56.3% girls) aged between 12 and 17 years from the Valle de Ricote (Region of Murcia, Spain). Chronotype was assessed using the Morningness/Eveningness Scale in Children (MESC). Disordered eating was evaluated by two psychologists using the Sick, Control, One, Fat, and Food (SCOFF) questionnaire. Results: Adolescents with an eveningness chronotype showed a higher SCOFF score (estimated marginal mean [M] = 1.1; 95% confidence interval [CI] 0.7 to 1.5) in comparison with adolescents with a morningness chronotype (M = 0.7; 95% CI 0.5 to 0.8) (p = 0.010), as well as with those with an intermediate chronotype (M = 0.6; 95% CI 0.5 to 0.8) (p = 0.032). A higher predictive probability of having disordered eating was identified in adolescents with an eveningness chronotype (39.5%; 95% CI 22.8% to 59.1%), compared to adolescents with an intermediate chronotype (14.9%; 95% CI 10.8% to 20.1%) (p = 0.008) and with their counterparts with a morningness chronotype (16.9%; 95% CI 11.6% to 24.0%) (p = 0.021). Conclusions: This study reveals that adolescents with an eveningness chronotype are more likely to exhibit disordered eating behaviors compared to those with morningness or intermediate chronotypes. These findings highlight the importance of considering chronotype in adolescent health, particularly in developing targeted interventions to prevent eating disorders.