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Introduction Burning mouth syndrome (BMS) is a complex orofacial pain disorder characterised by chronic intraoral burning or dysesthesia, typically occurring daily for more than 2 hours per day and persisting for over 3 months. The absence of identifiable causative lesions defines BMS, and symptoms may appear with or without accompanying somatosensory changes, such as altered taste or tactile sensations. This article outlines the development of a systematic review protocol to investigate the prevalence of micronutrient deficiency in patients with BMS and enhance our understanding of possible diagnoses and management of patients with this disorder.Methods and analysis This systematic review will include observational studies that assessed micronutrient levels (such as iron, folate, cobalamin, zinc and homocysteine) to identify which micronutrients are lower than the normal range in patients with BMS. A literature search will be conducted on 25 August 2025, using the following databases: MEDLINE, Embase, LILACS, Scopus, Web of Science and the grey literature. Key terms such as “Burning Mouth Syndrome”, “stomatodynia”, “glossopyrosis”, “micronutrients” and “vitamins” will be used in our search strategies. Experts in the topic and reference lists of included studies will also be consulted. Two independent reviewers will select the study using a two-phase process. Data collection will be performed by one author and cross-checked by another. The risk of bias assessment will be conducted following the JBI tool. Meta-analyses may be performed to analyse the proportion of patients with micronutrient deficiency for each micronutrient investigated.Ethics and dissemination This systematic review does not require ethical approval. On completion, it will be published in a peer-reviewed academic journal and presented at a conference.PROSPERO registration number CRD42024626960.