Over the last few decades, the time adolescents spend using electronic devices has increased significantly. The aim of this study was to evaluate the impact of screen time and physical activity on eating behaviour in adolescents. This study used the Physical Activity Questionnaire for Adolescents (PAQ-A) Malay version and the Dutch Eating Behaviour Questionnaire (DEBQ) Malay version methods with secondary students around the Klang Valley. The sampling technique used was purposive sampling. With parents' consent, an online survey was conducted among adolescent school children aged between 13 and 17 years during the COVID-19 pandemic in the Klang Valley, Malaysia. There were 372 respondents participating in this study. The results showed that 99.4% of them had more than 4 h screen time a day, and that 38.5% have more than three devices at home. Moreover, there was a significant mean difference in screen time for console games without a handheld device between male and female adolescents ( < 0.05). There was also a significant mean difference in the emotional, restricted and external eating behaviour scores between male and female adolescents ( < 0.001). There was a significant relationship between physical activity and the time duration spent on a television, telephone and laptop during weekends ( < 0.05). There was a significant relationship between eating behaviour and time spent watching television and using laptops during weekends ( < 0.05). Based on the moderation model, gender as a moderator variable indicated that there was a significant relationship between screen time and interaction screen time and gender with emotional eating ( < 0.001). Female adolescents had a stronger relationship between screen time and emotional eating compared to male adolescents ( < 0.05). Meanwhile, for physical activity level as a moderator variable, the results showed that there was a significant interaction between screen time and physical activity for emotional eating behaviour ( < 0.05). In conclusion, this study indicates that screen time was higher among female adolescents and significantly related to emotional eating behaviour. Therefore, the educational sector should emphasise the motivation of adolescents to engage in physical activity, reduce their screen time and eat healthy foods such as fruits and vegetables.