This was a mixed-methods study comprising a questionnaire-based survey, a qualitative study, and analysis of school newsletters to evaluate elementary school staff’s acceptability, delivery challenges and communication about school-located influenza vaccination program (SIVP) in Hong Kong. We found that school staff with lower intention to implement SIVP perceived greater logistical difficulties in arranging SIVP. Challenges regarding program delivery included schools’ limited infrastructure, the burden of paperwork, the fear of being overwhelmed by multiple school-based vaccination schedules, lacking confidence in communicating with parents about influenza vaccines, and the difficulties in managing vaccination-related anxiety among children with intellectual disability. School staff were generally passive in communicating with parents and students about influenza vaccines. We also found that schools may use the school newsletters as a substitute of the formal informed consent forms. Good partnerships among government, service providers and schools should be established to minimize the burden of paperwork for school staff, facilitate early planning of SIVP, and support schools with limited infrastructure and the vaccination of children with intellectual disabilities. Training is needed to enhance school staff’s confidence in communicating with parents and students about influenza vaccines and improve information delivery to support parents’ informed decisions for children’s vaccination.