Interest in the applications of music in health, social care and community settings are growing worldwide. Rare diseases are a major challenge for public health, particularly in paediatric populations. Previous research has demonstrated music and music medicine benefit children and young people’s health and wellbeing; however, this is under-researched in the paediatric rare disease context. This scoping review was conducted to explore music therapy and music medicine as tools to support children with rare diseases’ health and wellbeing within healthcare settings. The review investigated the current research on how music is used for children and young people with rare diseases and complex conditions and synthesised the resulting evidence. Results from this review suggest that music therapy and music medicine are beneficial for the health and wellbeing of children with rare diseases and complex conditions, including reduced anxiety, stress and pain during clinical procedures, and increased communication, social and coping skills and enhanced quality of life.