Background: To assess the event rates of myocarditis detected by Cardiac Magnetic Resonance (CMR) in athletes who recovered from COVID-19. Methods: A systematic literature search was performed to identify studies reporting abnormal CMR findings in athletes who recovered from COVID-19. Secondary analyses were performed considering increased serum high sensitivity troponin (hs-Tn) levels and electrocardiographic (ECG) and echocardiographic (ECHO) abnormalities. Results: In total, 7988 athletes from 15 studies were included in the analysis. The pooled event rate of myocarditis was 1% (CI 1–2%), reaching 4% in the sub-group analysis. In addition, heterogeneity was observed (I2 43.8%). The pooled event rates of elevated serum hs-Tn levels, abnormal ECG and ECHO findings were 2% (CI 1–5%), 3% (CI 1–10%) and 2% (CI 1–6%), respectively. ECG, ECHO and serum hs-Tn level abnormalities did not show any correlation with myocarditis. Conclusions: The prevalence of COVID-19-related myocarditis in the athletic population ranges from 1 to 4%. Even if the event rate is quite low, current screening protocols are helpful tools for a safe return to play to properly address CMR studies. Trial registration: the study protocol was registered in the PROSPERO database (registration number: CRD42022300819).