IntroductionAllergic rhinitis (AR) is a kind of widespread but unrecognised inflammatory disorder of nasal mucosa, characterised by itching, sneezing, runny nose and nasal congestion. The efficacy of mesenchymal stem cells (MSCs) in the treatment of AR remains controversial. This protocol describes a systematic review and meta-analysis approach to assess the efficacy and safety of MSCs in the treatment of AR.Methods and analysisEight databases (PubMed, Embase, Cochrane Library, Web of Science, China National Knowledge Infrastructure, Chinese Biomedical Literature Database, VIP and Wanfang) will be searched from the database inception to 1 December 2023. All randomised controlled trials related to MSCs for AR will be included. The primary outcomes will be therapeutic effect, serum IgE index and Visual Analogue Scale score for nasal symptoms. Risk of bias will be assessed using the Cochrane Collaboration’s tool for assessing risk of bias. Article selection, data extraction and risk of bias assessment will be performed in duplicate by two independent reviewers.Ethics and disseminationEthics approval is not required because individual patient data are not included. This protocol was registered in the international Prospective Register of Systematic Reviews on 22 January 2022. The systematic review and meta-analysis will be submitted for publication in a peer-reviewed journal. The findings will also be disseminated through conference presentations.PROSPERO registration numberCRD42022303146.