We conducted a test negative study from November 2023 to June 2024, enrolling 4,367 children hospitalized with acute respiratory illness in Hong Kong. Among the children who tested negative for influenza virus and SARS-CoV-2, 56.8 % had received influenza vaccination. Between November 2023 and March 2024, influenza A(H3N2) predominated and the VE against influenza A(H3N2) was estimated as 55 % (95 % CI: 29.6 %, 71.8 %). VE point estimates were higher for younger children than older children. In February to June 2024 influenza A(H1N1) predominated and VE against influenza A(H1N1) was 54 % (95 % CI: 33 %, 69 %) during this period. Influenza B/Victoria circulated at low intensity throughout the 2023/24 season and VE against influenza B was 66 % (95 % CI: 42 %, 80 %). Since its introduction in 2018/19 the school-based influenza vaccination program has substantially increased vaccine uptake in children in Hong Kong and prevented influenza-associated hospitalizations.