Abstract Background The SARS-CoV-2 Omicron BA.2 subvariant replaced BA.1 globally in early 2022, and caused an unprecedented tsunami of cases in Hong Kong, resulting in the collapse of elimination strategy. Vaccine effectiveness (VE) of BNT162b2 and CoronaVac against BA.2 is unclear. Methods We utilize an ecological design incorporating population-level vaccine coverage statistics and territory-wide case-level SARS-CoV-2 infection surveillance data, and investigate the VE against infection during the Omicron BA.2 wave between January 1 to April 19, 2022, in Hong Kong for children and adolescents. Results We estimate VE to be 33.0% for 1 dose of BNT162b2 in children aged 5–11 and 40.8% for 2 doses of CoronaVac in children aged 3–11. We also estimate 54.9% VE for 2 doses of BNT162b2, and 55.0% VE for 2 doses of CoronaVac in adolescents aged 12–18. Conclusions Our findings support partly preserved VE against infection by variants of concerns for children and adolescents in settings with extremely low levels of prior SARS-CoV-2 circulation.