Introduction – Burning mouth syndrome (BMS) is a rare disease of unknown origin. No efficient treatment is known, and integrative approaches are warranted. So far, individualised homeopathy (iHOM) has not been evaluated or reported in any peer-reviewed journal as a treatment option. Methods – At the Centre of Complementary Medicine at a university institute in Switzerland, a 38-year-old patient with BMS and various co-morbidities was treated with iHOM between July 2014 and August 2018. The treatment involved prescription of individually selected homeopathic single remedies. During follow-up visits, outcome was assessed with two validated questionnaires concerning patient-reported outcomes. To assess whether the documented changes were likely to be associated with the homeopathic intervention, an assessment using the modified Naranjo criteria was performed. Results – Over an observation period of 4 years, an increasingly beneficial result from iHOM was noted for oral dysaesthesia and pains as well as for the concomitant symptoms. Conclusion – Considering the multi-factorial aetiology of BMS, a therapeutic approach such as iHOM that integrates the totality of symptoms and complaints of a patient might be of value in cases where an association of psychological factors and the neuralgic complaints is likely.