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Background: The impact of long-term Coronavirus disease 2019 (COVID-19) on the pediatric population is still not well understood. This study was designed to estimate the magnitude of COVID-19 long-term morbidity 3–6 months after the date of diagnosis. Methods: A retrospective study of all Clalit Health Services members in Israel aged 1–16 years who tested positive for SARS-CoV-2 between April 1, 2020 and March 31, 2021. Controls, who had no previous diagnosis of COVID-19, were one-to-one matched to 65,548 COVID-19-positive children and teens, and were assigned the infection dates of their matches as their index date. Matching included age, sex, socio-economic score, and societal sector. Individuals were excluded from the study if they had severe medical conditions before the diagnosis such as cancer, diabetes, chronic respiratory diseases, and/or abnormal physiological development. Generalized Estimating Equations were used to estimate the associations between COVID-19 and the use of medical services. The analysis focused on the 3–6 months after the infection date. Adjustments were made for demographics and for the use of medical services 6–12 and 3–6 months before the infection date. The latter was necessary because of observed disparities in medical service utilization between the groups before the COVID-19 diagnosis, despite the matching process. Results: Statistically significant differences were only found for referrals for mental health services [adjusted relative-risk (RR) 1·51, 95%CI 1·15 − 1·96; adjusted risk-difference (RD) 0·001, 95%CI 0·0006 − 0·002], and medication prescriptions of any kind (RR 1·03, 95%CI 1·01–1·06; RD 0·01 95%CI 0·004 − 0·02). Conclusions: The significant increase in medication prescriptions and mental health service referrals support the hypothesis that COVID-19 is associated with long-lasting morbidities in children and adolescents aged 1–16 years. However, the risk difference in both instances was small, suggesting a minor impact on medical services. [ABSTRACT FROM AUTHOR]