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Background: The long-term sequela of COVID-19 on young people is still unknown. This systematic review explored the effect of COVID-19 on lung imaging and function, cardiorespiratory symptoms, fatigue, exercise capacity and functional capacity in children and adolescents ≥ 3 months after infection. Methods: A systemic search was completed in the electronic databases of PubMed, Web of Science and Ovid MEDLINE on 27 May 2022. Data on the proportion of participants who had long-term effects were collected, and one-group meta-analysis were used to estimate the pooled prevalence of the outcomes studied. Results: 17 articles met the inclusion criteria, presented data on 124,568 children and adolescents. The pooled prevalence of abnormalities in lung imaging was 10% (95% CI 1–19, I² = 73%), abnormal pulmonary function was 24% (95% CI 4–43, I² = 90%), chest pain/tightness was 6% (95% CI 3–8, I² = 100%), heart rhythm disturbances/palpitations was 6% (95% CI 4–7, I² = 98%), dyspnea/breathing problems was 16% (95% CI 14–19, I² = 99%), and fatigue was 24% (95% CI 20–27, I² = 100%). Decreased exercise capacity and functional limitations were found in 20% (95% CI 4–37, I² = 88%) and 48% (95% CI 25–70, I² = 91%) of the participants studied, respectively. Conclusion: Children and adolescents may have persistent abnormalities in lung imaging and function, cardiorespiratory symptoms, fatigue, and decreased functional capacity between 3 to 12 months after infection. More research is needed to understand the long-term effect of COVID-19 on young people, and to clarify its causes and effective management.