Rare neurological conditions (RNCs) encompass a variety of diseases that differ in progression and symptoms but typically include muscle weakness, sensory and balance impairment and difficulty with coordinating voluntary movement. This can limit overall physical activity, so interventions to address this are recommended. The aim of this study was to agree a core outcome measurement set for physical activity interventions in people living with RNCs. We followed established guidelines to develop core outcome sets. Broad ranging discussions in a series of stakeholder workshops led to the consensus that (1) physical well-being; (2) psychological well-being and (3) participation in day-to-day activities should be evaluated in interventions. Recommendations were further informed by a scoping review of physical activity interventions for people living with RNCs. Nearly 200 outcome measures were identified from the review with a specific focus on activities or functions (e.g, on lower limb function, ability to perform daily tasks) but limited consideration of participation based outcomes (e.g., social interaction, work and leisure). Follow on searches identified two instruments that matched the priority areas: the Oxford Participation and Activities Questionnaire and the Sources of Self-Efficacy for Physical Activity. We propose these scales as measures to assess outcomes that are particularly relevant to assess when evaluating physical activity interventions mong people with RNCs. Validation work across rare neurological conditions is now required to inform application of this core outcome set in future clinical trials to facilitate syntheses of results and meta-analyses.