Background: Both eating disorders and excessive internet use represent significant health issues for contemporary adolescents. Yet, the link between them has seldom been investigated. We aim to study this association through their common underlying psychological factors: internalising problems and externalising problems. Methods: A representative sample of 7,083 adolescents (Mage = 13.48 years; SDage = 1.32; 50.3% girls) from Slovakia was obtained from the Health Behaviour in School-aged Children (HBSC) project in 2018. Study variables included the Excessive Internet Use Scale (EIU) and the Strength and Difficulties Questionnaire (SDQ). Eating disorders symptoms (EDS) were assessed by SCOFF and selected items from the Eating Disorder Screen for Primary Care (ESP). Data were analysed separately for boys and girls with Structural Equation Modelling. Results: There was a partial correlation between EDS and EIU (r = 0.36 for boys and r = 0.29 for girls) after controlling for the internalising and externalising of problems. Internalising and externalising problems were positively associated with EDS, while EIU was only associated with externalising problems. The results were comparable for both genders. Conclusion: The study provides evidence that, during adolescence, EDS and EIU are related and have a tendency to occur together. Also, they are related even when controlled for their shared underlying psychological factors, namely the emotional and attentional/behavioural difficulties.