With the SARS-CoV-2 pandemic, the impact of recent coronavirus, especially in children, cannot be ignored. In this study, we evaluated the SARS-CoV-2 infection rates and associated features in children less than 18 years of age in “Fars” and “Kohgiluyeh and Boyer Ahmad”, provinces, Iran. 5943 children who were suspected cases to SARS-CoV-2 infection were enrolled in this study. Demographic and clinical data of SARS-CoV-2 patients were collected from 16 February 2020 to 20 June 2021. Underlying conditions were considered in this study as well. Among 5943 patients suspected COVID 19 cases, 13.51% were confirmed by real-time PCR assay. The female/male ratio was 1:1.3 with a mean age of 5.71 years. 11.2% of confirmed patients were transferred and admitted in Pediatric ICU. COVID 19 was significantly higher in children with malignancy and diabetes rather than those with other underlying diseases. Children of all ages were susceptible to COVID 19, and there is no significant difference between both sexes. Most of the COVID 19 cases were in 10–18 years old group. Among a number of children with different underlying diseases, children with malignancy had the highest rate of SARS-CoV-2 infection, followed by those with diabetes.