Abstract: Influenza-like illness (ILI) outbreaks mainly occurred in schools. And annually reformulated composition of influenza vaccines makes it necessary to estimate the effectiveness of the seasonal influenza vaccine. We aimed to estimate the effectiveness of the seasonal influenza vaccine against influenza outbreaks in schools. Methods This was a matched case-control study estimating the effectiveness of the influenza vaccine in preventing school influenza outbreaks. The laboratory-confirmed cases of influenza in school children were paired by the random sample of asymptomatic classmates by sex and age during the 2019–2020 influenza season. Influenza vaccine effectiveness was estimated using a conditional logistic regression model. Results During the 2019–2020 influenza season, 503 paired samples of laboratory-confirmed influenza cases and asymptomatic controls were enrolled. The influenza vaccination rates for cases and controls were 0.40% and 1.59%, respectively. The vaccine effectiveness against influenza outbreaks in schools was 74.35% (95% CI: 5.39–122.00) during the 2019–2020 season. Conclusions No significant vaccine effectiveness was observed during influenza outbreaks in schools during the 2019–2020 influenza season because of the low vaccination rate. Efforts should be made to increase vaccination coverage among students.