Objective To understand the influenza (flu) vaccination status and willingness and influencing factors among students in primary and secondary schools with flu outbreaks in Sichuan province and provide reference for formulating flu vaccination strategies.

Methods This study was conducted in 7 primary and secondary schools where flu outbreaks occurred from February to April 2023 in Sichuan province. A total of 5 373 primary and secondary school students in classes with ≥ 2 confirmed cases of flu were selected by convenient sampling method for a questionnaire survey. To reveal the flu vaccination status in the 2020–2023 flu season and the willingness to receive flu vaccination in the 2023–2024 flu season, we employed multivariate unconditional logistic regression to analyze the influencing factors of flu vaccination willingness.

Results Among the 4 718 primary and secondary school students included in the analysis, 1 320 (28.0%) received flu vaccination in any season during the 2020–2023 flu season. Among them, the flu vaccination rates in the 2020–2021, 2021–2022, and 2022–2023 flu seasons were 10.4% (491/4 718), 14.0% (658/4 718), and 16.6% (785/4 718), respectively. The flu vaccination rates varied in different flu seasons (χ² = 77.076, P < 0.001). The primary motivations for parental consent to flu vaccination included awareness of vaccine benefits leading to a desire for comprehensive protection (60.5%), concern about severe influenza outbreaks and infection risk (12.9%), and school teacher recommendations (9.9%). Conversely, the main reasons for vaccine hesitancy were lack of knowledge about vaccine availability or annual vaccination requirements (33.5%), concerns about potential adverse reactions (21.2%), and perceived risk of post-vaccination infection (10.8%). During the 2023–2024 flu season, 4 113 (87.2%) students expressed willingness to receive flu vaccination. Multivariate logistic regression analysis identified that primary and secondary school students residing in City A and City B, receiving flu vaccination during the 2020–2023 flu season, being aware of annual vaccination requirements, believing in vaccination’s protective efficacy against infection, and concerning about potential transmission from infected classmates and friends demonstrated higher vaccination willingness. Conversely, students aged ≥ 16 years, secondary school attendees, residents of City B, and those concerned about adverse reactions showed lower vaccination willingness.

Conclusions The flu vaccination coverage among students in primary and secondary schools affected by flu outbreaks in Sichuan province remained suboptima during the 2020–2023 flu seasons. However, vaccination willingness was higher in the 2023–2024 flu season. Key determinants of vaccination willingness included age and city of residence, vaccination history in the 2020–2023 flu seasons, awareness of annual vaccination requirements, perceived efficacy in reducing infection risk, concerns about adverse reactions, and apprehension regarding disease transmission from peers.