SARS-influence CoV-2’s on children was initially unknown. Real-time qPCR confirms COVID-19 diagnosis. RT-qPCR cycle threshold (Ct) values are inversely proportional to viral load and indirectly measure viral Ribonucleic acid (RNA) copy numbers. This study aimed to examine the relationship between COVID-19 epidemiology, clinical features, and Ct values. Cross-sectional, observational analysis. All COVID-19 children under 18 were admitted to Ricardo Gutiérrez Children’s Hospital between March 1, 2020, and February 28, 2021. RT-qPCR confirmed SARS-CoV-2. 7-year-olds were the median age. In 419 cases, the median Ct was 23.5 [Interquartile range (IQR): 18.9–30.9]. Levels were lower in symptomatic than asymptomatic individuals (Ct: 22.1; IQR: 18.4–22.1), in children less than 2 years old (Ct: 20.6; IQR: 17.3–27.3), and when sample collection was less than 4 days following symptom onset (Ct: 21.1; IQR: 18.1–27.5). Symptomatic children more than 2 years old had lower Ct levels than asymptomatic children (Ct: 22.6; IQR: 18.7–29.3). Younger COVID-19 patients have lower Ct values, indicating a larger viral load. Symptomatic toddlers had lower Ct values than asymptomatic toddlers.