The emergence of COVID-19 (SARS-CoV-2) has presented public health professionals with new challenges in the diagnosis of the disease and treatment of patients. Nowadays, the epidemiology, clinical features, prevention and treatment of the disease are studied poorly due to continuous mutation of the pathogen. One of the consequences of the new coronavirus infection could be changes in the immune system of the human population. A detailed analysis of the immunological status of different racial groups under the influence of the new coronavirus infection is currently studied insufficiently, making this work of particular relevance. There is also a reluctance among some Russian residents to be vaccinated, including the population of Perm Krai, due to a lack of research on possible deviations in cellular immunity due to SARS-CoV-2 vaccination. At the start of the third wave caused by the new coronavirus infection, only 40% of the Russian population had been vaccinated, which was insufficient to acquire collective immunity. In the autumn of 2021, a QR code measure was introduced for vaccinated residents, which resulted in exceeding the necessary barrier for acquiring collective immunity. Due to the high growth and severity of the disease, we analysed the immunograms of children and adolescents, aged from 5 months to 17 years, in Perm Krai during the pandemic years 2020–2021. The patients’ immunological status results were divided into three categories. Laboratory diagnosis of the human immune system was carried out using serological and flow cytophotometric analyses. A total of 247 samples were analysed. The aim of this work was to investigate changes in the immune system of children and adolescents during the pandemic caused by the new coronavirus infection. The methodology was based on the analysis of immunograms, including biochemical studies, immune status and flow cytophotometric analysis. The immunograms were pre-sorted by IgA, IgM, IgG immunoglobulin status into four categories: absence of disease—k1 in which IgA, IgM, IgG immunoglobulin values were within the reference interval, active disease stage—k2 in which IgA, IgM immunoglobulins had gone beyond the reference interval, passive disease stage—k3 characterised by IgG and IgM immunoglobulin status, and patient recovery process—k4. In the immunograms, three immune status indicators were selected for further investigation: phagocytosis absolute value, phagocytic number and phagocytic index and five flow cytometry indices: leukocytes, lymphocytes, NK cells (CD16+CD56+), T helpers (CD3+CD4+) and CD4+/CD8+ immunoregulation index. A quantitative analysis of the deviations of these indicators from the reference intervals was performed in the three studied age groups of children and adolescents living in Perm Krai of the Russian Federation during the pandemic of 2020–2021.