Background: this study aimed to estimate the economic impact and health-related quality of life (HRQOL) of patients with spinal muscular atrophy (SMA) in three European countries. It was used a cross-sectional study carried out in France, Germany, and the United Kingdom. Data were collected from July 2015 to November 2015. Healthcare costs (hospitalizations, emergencies, medical tests, drugs used, visits to general practitioners (GPs) and specialists, medical material and healthcare transport), and non-healthcare costs (social services and informal care) were identified and valued. EuroQol instruments, the Zarit interview, and the Barthel Index were also used to reflect the burden and the social impact of the disease beyond the cost of healthcare. Results: we included 86 children with SMA, 26.7% of them had Type I, and 73.3% Type II or III. The annual average cost associated with SMA reaches €54,295 in the UK, €32,042 in France and €51,983 in Germany. The direct non-healthcare costs ranged between 79–86% of the total cost and the informal care costs were the main component of these costs. Additionally, people suffering from this disease have a very low health-related quality of life, and there are large differences between countries. Conclusions: SMA has a high socioeconomic impact in terms of healthcare and social costs. It was also observed that the HRQOL of affected children was extremely reduced. The figures shown in this study may help to design more efficient and equitable policies, with special emphasis on the support provided to the families or on non-healthcare aid.