The associations of COVID-19 with Kawasaki disease (KD) and multisystem inflammatory syndrome in children (MIS-C) remain unclear. Few large-scale studies have estimated the cumulative incidence of MIS-C and KD after COVID-19 in children. Data were obtained from TriNetX. After propensity score matching was completed, data from 258,645 patients with COVID-19 (COVID-19 group) and 258,645 patients without COVID-19 (non-COVID-19 group) were analyzed using Cox regression. Hazard ratio (HR), 95% confidence interval (CI), and cumulative incidence of MIS-C and KD were calculated for both groups. Stratified analysis was performed to validate the results. After matching for age at baseline and sex, the risks of MIS-C and KD were higher in the COVID-19 group than in the non-COVID-19 group (HR: 3.023 [95% CI: 2.323 to 3.933] and 1.736 [95% CI: 1.273 to 2.369], respectively). After matching for age at baseline, sex, race, ethnicity, and comorbidities, the risks of MIS-C and KD remained significantly higher in the COVID-19 group than in the non-COVID-19group (HR: 2.899 [95% CI: 2.173 to 3.868] and 1.435 [95% CI: 1.030 to 2.000]). When stratified by age, the risk of MIS-C was higher in the COVID-19 group-for patients aged > 5 years and ≤ 5 years (HR: 2.399 [95% CI: 1.683 to 3.418] and 2.673 [95% CI: 1.737 to 4.112], respectively)-than in the non-COVID-19 group. However, the risk of KD was elevated only in patients aged ≤ 5 years (HR: 1.808; 95% CI: 1.203 to 2.716). When stratified by COVID-19 vaccination status, the risks of MIS-C and KD were elevated in unvaccinated patients with COVID-19 (HR: 2.406 and 1.835, respectively). Patients with COVID-19 who are aged < 18 and ≤ 5 years have increased risks of MIS-C and KD, respectively. Further studies are required to confirm the role of COVID-19 in the pathogenesis of MIS-C and KD.