This study aimed to investigate anxiety, depression levels, and emotional/behavioral problems of children and adolescents while being treated in the COVID-19 unit. The present study included 50 children who were COVID-19 positive, aged 7–18 years, and 50 age- and gender-matched healthy controls. The sociodemographic data form and Revised Child Anxiety and Depression Scale–Child Version (RCADS-C) were applied to all children, and all families were asked sociodemographic data form, Revised Child Anxiety and Depression Scale–Parent Version (RCADS-P), and Strengths and Difficulties Questionnaire (SDQ). There was no significant difference between the patient and control groups in terms of anxiety, depression levels, and emotional/behavioral problems. The conduct problems subscale score of SDQ in the patient group was found to be significantly lower than the control group (p = 0.037). Separation anxiety subscale scores of RCADS (p = 0.034) and the rate of accompanying companions (p = 0.01) in the patient group were found to be significantly higher in preadolescents than in adolescents. In conclusion, this study demonstrated that children and adolescents who were COVID-19 positive were not different from healthy children in terms of anxiety and depression levels, and emotional and behavioral problems in the acute period during inpatient treatment.