Detailed data on clinical characteristics in children with the omicron strain of SARS-COV-2 are limited. We conducted a retrospective observational study of children with COVID-19 at the National Center for Child Health and Development to evaluate the clinical manifestations during and before the emergence of the omicron variant. Only symptomatic patients without underlying diseases were included. Participants were divided into two temporal groups: the “omicron era” (1/2022–2/2022) and the “pre-omicron era,” where the delta variant predominated (7/2021–11/2021). The patients were subclassified into an older vaccine-eligible group (aged 12–17 years), a younger vaccine-eligible group (aged 5–11 years), and a vaccine-ineligible group (aged 0–4 years). We compared 113 patients in the omicron era with 106 in the pre-omicron era. Most patients in both eras had non-severe disease, and no patients required mechanical ventilation or died. Among patients aged 0–4 years, sore throat and hoarseness were more common during the omicron era than the pre-omicron era (11.1% vs. 0.0% and 11.1% vs. 1.5%, respectively). Croup syndrome was diagnosed in all patients with hoarseness. Among patients aged 5–11 years, vomiting was more frequent during the omicron era (47.2%) than during the pre-omicron era (21.7%). Cough and rhinorrhea were less common during the omicron era in patients aged 0–4 and 5–11 years, respectively, than during the pre-omicron era. In children with COVID-19, clinical manifestations differed between the omicron and pre-omicron eras. In the Omicron era, croup syndrome was more frequent in vaccine-ineligible children.