The fifth wave of the coronavirus disease 2019 (COVID-19) pandemic in Hong Kong was dominated by the Omicron variant, which may cause more upper airway involvement in children. This study was performed to identify any associations between the Omicron variant of COVID-19 and croup in children. This retrospective study reviewed the electronic medical records of patients admitted to Tuen Mun Hospital in Hong Kong from 1 January 2018 to 31 March 2022 under the diagnostic code for croup (J05.0 in the International Classification of Diseases 10th Edition). Patients were categorised into three groups according to their admission periods, namely, non-COVID-19, COVID-19-pre-Omicron, and COVID-19-Omicron groups. Disease associations and severity were compared according to incidence, Westley Croup Score, length of hospital stay, medication use, respiratory support, and intensive care unit admissions. The COVID-19 incidence among patients with croup was significantly higher in the COVID-19-Omicron group than in the COVID-19-pre-Omicron group (90.0% vs 2.0%; P<0.001). Compared with patients in the COVID-19-pre-Omicron and non-COVID-19 groups, patients in the COVID-19-Omicron group also had a higher Westley score (moderate and severe disease in the COVID-19-Omicron group: 56.7%; COVID-19-pre-Omicron group: 22.0%, P=0.004; non-COVID-19 group: 24.8%, P<0.001), longer median hospital stay (COVID-19-Omicron group: 3.00 days; COVID-19-pre-Omicron group: 2.00 days, P<0.001; non-COVID-19 group: 2.00 days, P=0.034), and higher mean dexamethasone requirement (COVID-19-Omicron group: 0.78 mg/kg; COVID-19-pre-Omicron group: 0.49 mg/kg, P<0.001; non-COVID-19 group: 0.58 mg/kg, P=0.001). The Omicron variant of COVID-19 is associated with croup and can cause more severe disease in Hong Kong children.