Fukuyama congenital muscular dystrophy (FCMD) is the second most common childhood-onset muscular dystrophy in Japan. However, only a few comprehensive studies have investigated cardiac complications associated with FCMD, with none on arrhythmias. The present study evaluated 78 Holter electrocardiograms from 15 patients with FCMD. No patient developed fatal arrhythmia complications, but older patients tended to have increased premature ventricular contractions (PVCs). Besides age, no risk factors were found to be associated with the presence or absence of PVCs. The average heart rate over 24 h tended to be higher in patients with FCMD than in healthy young people. Moreover, some time domain variables of heart rate variability tended to decrease from the early stages of the disease, suggesting that autonomic nervous system function might have been impaired prior to the appearance of PVCs. FCMD is a progressive disease, with affected patients suffering from increased rates of PVCs over time, which can reflect cardiac dysfunction.