Background: The COVID-19 pandemic has caused a significant global burden. The paediatric population constituted the least percentage of confirmed cases of COVID-19, However, the distribution of infection cases among children in Iraq is unknown. Aims: Exploring the epidemiological profile of COVID-19 infection in children during the second and third waves. Methods: Electronic medical records were used to obtain COVID-19 data from January 2021 to December of the same year. The data included samples from positive cases of suspected cases referred to the Coronavirus Screening Centre/Public Health Laboratory, as part of the COVID-19, Hepatitis, AIDS and Syphilis screening programme in Diyala Governorate. The study included 1326 children aged 1-14 years. All suspected cases were examined based on the appearance of symptoms using RT-PCR. Results: A total of 907 (68.4%) children were confirmed during the second wave compared to 419 (31.6%) cases in the third wave. In terms of age, young adolescents, aged 10-14 years, showed a significantly higher susceptibility to infection. The distribution of COVID-19 cases by gender shows that the rate of male children with COVID-19 was 60.2% (n=800), significantly higher than female children 39.6% (n=526). The peak increase in COVID-19 cases was observed during March and April with 242 cases (18.2%) and 211 cases (15.9%) during the second wave, while the peak of the third wave was in July with 183 cases (13.8%) reported and confirmed Conclusion: We found a significant increase in paediatric infections during the Alpha variant period of the pandemic (March-April / 2021), with another increase during the first outbreak of the delta variant (July / 2021). Adolescents showed an increased susceptibility to COVID-19. Therefore, future preparedness for outbreaks of viral diseases such as COVID-19 and other pandemics requires officials and decision makers in health institutions to include all children in vaccination programs.