This article systematically examines the significance, ethical challenges and governance pathways of brain-computer interfaces (BCIs) in the field of sports medicine. As a core technology enabling the high-quality development of sports medicine, BCIs play a vital role in monitoring neural dynamics, decoding motor intentions and assessing neural characteristics. However, the application of BCIs in sports medicine still harbours ethical challenges, including data privacy breaches, the erosion of the subject’s autonomy, threats to life and health, and ambiguity regarding liability. In light of this, the paper proposes governance pathways including the establishment of a robust data governance system, the safeguarding of the subject’s autonomy, the reinforcement of safeguards for life and health, and the clarification of boundaries regarding rights and responsibilities. Furthermore, it outlines specific measures for integrating brain-computer interfaces into sports medicine across the ‘prevention–process–prognosis’ stages, thereby promoting the development of brain-computer interfaces in a regulated and efficient manner.