Hypertrophic cardiomyopathy (HC) is the most common genetic heart disease. Consensus guidelines recommend restriction from competitive and/or high-intensity physical activities; however, sufficient light-moderate intensity physical activity remains important for health and wellbeing. This study aimed to evaluate the effectiveness and appeal of a control theory-based intervention to increase physical activity levels in individuals with HC. A pre to post trial of HC participants (n = 25) recruited from May 2016 to April 2017 from a specialized, multidisciplinary clinic was conducted. A 12-week intervention based on principles of control theory was developed. The primary outcome measures were self-reported leisure and transport-related physical activity. The mean age of participants was 42 ± 13years and the majority were men (n = 15, 60%). Although both the primary (self-report) and secondary (objective) outcome measures of physical activity increased, such as leisure-time physical activity: 98 ± 132 minutes per week to 151 ± 218 minutes per week, these were not statistically significant. Secondary outcome measures improved, including physical health-related quality of life (HR-QoL; 43 ± 6 to 50 ± 8, p = 0.004), self-efficacy (14 ± 3 to 16 ± 4, p <0.001), and the number of barriers identified (4 ± 3 to 3 ± 2 barriers, p = 0.02). This simple, easy-to-administer intervention to promote physical activity in HC improved willingness to undertake physical activity, increased self-efficacy, and improved physical quality of life. This may help patients overcome perceived barriers and a lack of confidence regarding physical activity, with the ultimate goal to improve overall health outcomes in HC patients.