Spinal muscular atrophy (SMA) is a rare neuromuscular disease characterized by degeneration of the anterior horn cells of the spinal cord and motor nuclei in the lower brainstem, resulting in hypotonia, progressive proximal muscle weakness, paralysis, and progressive respiratory insufficiency. We report the case of a 6-year-old girl diagnosed with spinal muscular atrophy type 1 (Werdnig-Hoffman disease) who has been treated at home with non-invasive ventilation (assist-control mode with a back-up respiratory rate of 26 per minute). She presented with an atrioventricular block and atrial fibrillation, as well as paroxysmal fluctuation of blood pressure and heart rate indicating autonomic dysfunction. Although it is known that patients with spinal muscular atrophy type 1 do not generally demonstrate cardiac problems, it can be concluded based on findings in our case that long-term survivors with spinal muscular atrophy type 1 may develop cardiac rhythm disturbances. We therefore recommend that the possibility of cardiac complications and autonomic dysfunction should be borne in mind in the management of such patients.