We carried out an observational, retrospective and descriptive study in order to identify the clinical and epidemiological characteristics of children with SARS-CoV-2 infection admitted to a Peruvian national referral hospital. We included patients from one month old to fourteen years old hospitalized between March and August 2020. A total of 125 patients with SARS-CoV-2 infection were admitted, 18.4% (n = 23) had critical illness and 16.8% (n = 21) had multisystem inflammatory syndrome (MIS-C). The absence of comorbidities and previous history of epidemiological contact were more frequent in patients with MIS-C. Patients in critical condition and patients with MIS-C had lower lymphocyte and platelet counts, and higher C-reactive protein, ferritin and D-dimer values than patients who did not have said conditions. Six (4.8%) out of 125 children died, as well as 3 (13%) children from the group of patients in critical condition. None of the children with MIS-C died.