Background: The lack of SARS-CoV-2 antigen surveillance testing in the pediatric population has inhibited accurate infection and hospitalization prevalence estimates. We aim to report the estimated prevalence of and risk factors for COVID-19 infection, hospitalization, and intensive care unit (ICU) admission across the three United States (US) waves in one of the largest pediatric healthcare systems in the nation. Methods: Retrospective electronic health record (EHR) review of all COVID-19 surveillance data among children aged 0–19 years seeking healthcare at one pediatric healthcare system that serves predominantly Medicaid-dependent families from 1 March 2020 to 31 March 2021. COVID-19 infection status (Y/N), hospital admission (Y/N), and ICU admission (Y/N) are the main outcomes. Results: Of 22,377 children aged ≤ 19 years tested for SARS-CoV-2 infection from March 2020–March 2021, 3126 were positive (14.0%), and out of those positive, 53.7% were hospitalized and 2.9% were admitted to the ICU. Compared to Wave 1 (1 March 2020–31 May 2020), the risk of a positive test increased from 16% (RR 1.16, 95% CI, 1.07–1.26) in Wave 2 (1 June 2020–31 October 2020) to 33% (RR 1.33, 95% CI, 1.23–1.44) in Wave 3 (1 November 2020–31 March 2021). Similarly, compared to Wave 1, the risk for hospitalization increased 86% (RR 1.86, 95% CI, 1.86–2.06) in Wave 2 and 89% in Wave 3 (RR 1.89, 95% CI, 1.70–2.08), and the risk for ICU admission increased from 10% in Wave 2 (RR 1.10, 95% CI, 0.39–3.01) to 310% in Wave 3 (RR 3.10, 95% CI, 1.21–7.80). Children with asthma, depressive disorders, type 1 or 2 diabetes, and anemia were more likely to be hospitalized while children with diabetes, obesity, cardiac malformations, and hypertension were more likely to be admitted to the ICU versus children without these conditions. Conclusions: Children were cumulatively impacted by the COVID-19 pandemic through the three US waves with more than a third hospitalized in Wave 3. Children with underlying health conditions were particularly at risk for severe illness and should be monitored for any long-term impacts.