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Introduction Oral mucositis is a highly prevalent condition in individuals treated for haematological neoplasms, primarily during haematopoietic stem cell transplantation (HSCT). The condition is known to delay recovery processes, increasing the risk of infection, the number of interventions and the length of hospital stays. The proposed Photobiomodulation Therapy for Oral Mucositis and Functional Impairment Transplantation Trial aims to assess the effectiveness and acceptability of using photobiomodulation in the oral cavity to prevent oral mucositis and functional impairment in adult patients undergoing HSCT.Methods and analysis This is an assessor-blinded and statistician-blinded, parallel-group randomised controlled clinical trial (photobiomodulation vs control group). Participants and setting: 30 patients, aged 18–65 years, with haematological neoplasms undergoing HSCT at the Clínica Dávila Oncology and Bone Marrow Transplant Unit. Primary outcome measures: oral mucositis will be assessed daily using the WHO grading scale, beginning on the day of transplant through day 20 post-transplant. Researchers will assess functional capacity using a 2 min step test, handgrip strength with the Jamar digital dynamometer, lower limb strength using a 30’ sit-to-stand test and quality of life with the Functional Assessment of Cancer Therapy-Bone Marrow Transplantation Questionnaire. Acceptability will be assessed by logging treatment adherence and using a Visual Analogue Scale. Assessments will occur at two time points (1): on admission to the transplant unit, before starting the conditioning regimen and (2) on the day of discharge. Intervention: three times per week photobiomodulation therapy using a diode laser device will begin the first day of conditioning and continue through day 3 post-transplant.Ethics and dissemination The Clínica Dávila and Universidad del Desarrollo Clinical Research Ethics Committees approved this study in accordance with the Helsinki Declaration. Patients’ informed consent will be required. The dissemination strategy includes publication in scientific journals as well as presentations in the media and at conferences.Trial registration number NCT06260111.