Only a few studies have examined the effects of coronavirus disease 2019 (COVID-19) and influenza on clinical outcomes in pediatric patients. Furthermore, no meta-analysis has assessed the impact of these diseases on adverse outcomes. This study aims to compare the clinical outcomes of COVID-19 and influenza in pediatric patients. Searches were conducted from December 2019 to February 2022 in databases including Embase, Scopus, PubMed Central (PMC), MEDLINE, Google Scholar, Cochrane Library, and ScienceDirect. Our meta-analysis used a random-effects model, reporting pooled odds ratios (ORs) or standardized mean differences with 95% confidence intervals (95% CIs). Thirteen studies meeting the inclusion criteria were analyzed. Most studies had poor quality. The pooled OR was 0.13 for oxygen requirement (95% CI: 0.04-0.45; I2 = 74%) and 0.03 for steroid requirement (95% CI: 0.01-0.19; I2 = 60.8%). No significant differences were found in outcomes such as intensive care unit (ICU) admission, duration of inpatient stay, invasive/non-invasive ventilation, death, acute respiratory distress syndrome (ARDS), and acute kidney injury (AKI). SARS-CoV-2 infection was comparable to influenza regarding mortality, pediatric intensive care unit (PICU) admissions, mechanical ventilation, and AKI incidence, but with notable differences in oxygen supplementation.