Introduction The mechanisms generating immunity involved in nasal vaccination for children are likely to differ significantly from both adult immunity and animal models. A deeper understanding is necessary for the development of future paediatric mucosal vaccines. Live-attenuated influenza vaccines (LAIVs) are licensed mucosal vaccines which confer protection in children against severe influenza. Beyond individual protection, mucosal vaccines can also limit transmission and colonisation, offering broader public health benefits than parenteral vaccination. We describe a protocol for an exploratory, observational study assessing systemic and mucosal responses to LAIV in healthy children. Methods and analysis 40 healthy participants aged 2–5 years inclusively will be recruited from the community. Researchers will conduct study visits in the participants’ homes and administer a single dose of their routine, yearly LAIV and collect blood, nasal cells, nasal fluid and saliva at baseline and at day 28 post-LAIV. They will have additional nasal fluid and saliva samples conducted by caregivers on days 1, 2, 3, 4, 6, 9, 14 and 21. They will complete a daily symptom report to detect symptoms due to vaccination as well as additional upper respiratory illnesses. Samples will be analysed to detect viral load for influenza virus strains included in LAIV, coinfection and colonisation by other pathogens, as well as assess the mucosal and systemic immune response to vaccination. This study aims to advance understanding of mucosal immunity mechanisms in children following live-attenuated influenza vaccination. This knowledge could help inform the development of future mucosal vaccines for children, potentially increasing both effectiveness, ease of delivery and tolerability in this vulnerable population. Ethics and dissemination This protocol has been reviewed by the sponsor, collaborators and external peer reviewers. Ethical approval for this study has been obtained from the South Central - Hampshire B Research Ethics Committee (REC ref 24/SC/0251). Informed parental consent will be obtained prior to any study intervention. The results will be disseminated via publication in a peer-reviewed journal and presentation at international conferences. Study registration ISRCTN87260269 ( https://doi.org/10.1186/ISRCTN87260269 ).