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(1) Background: Eating disorder risk factors in children are early maturation, body dissatisfaction, dieting, stress and physical inactivity. The COVID-19 pandemic has further exacerbated these factors due to isolation, online classes and reduced physical activity, all of which have increased children's risk of developing eating disorders. The aim of the research was to examine the frequency of eating disorders among school-aged children in the Republic of Serbia during the COVID-19 pandemic, as well as the association of these disorders with socio-demographic characteristics, lifestyle habits, and levels of depression, anxiety and stress. (2) Methods: The research was conducted as a descriptive cross-sectional study on a sample of students from the fifth grade of elementary school to the fourth year of secondary school. The research was conducted from May to August in 2023. using the EAT-26 questionnaire. Before the research, the approval of the ethics committee of the Jagodina Health Center (No. 1238/28.04.2023.) was obtained, where the research was conducted. (3) Results: The results show that 5.8% of students exhibited eating disorder symptoms during the COVID-19 pandemic (EAT-26 ≥ 20). Statistically significant differences were observed in girls with an eating disorder, who had a significantly lower body weight compared to the others (<i>p</i> < 0.05). Students with symptoms of depression, anxiety and stress showed eating disorders significantly more often. Also, elementary school students and boys with an eating disorder visited a nutritionist and played sports more often. (4) Conclusions: Research has shown that during the COVID-19 pandemic, a smaller percentage of students showed symptoms of eating disorders, with girls being more sensitive. Disorders were significantly associated with the presence of depression, anxiety and stress. The obtained results indicate the importance of monitoring children's psychological and nutritional health, as well as the need for preventive and intervention measures in crisis conditions.