BACKGROUND: The present study aimed to clarify the relationship between high physical activity (PA) and function of the autonomic nervous system, which is important in the prognosis after stroke. We hypothesized a positive association between PA and the very low-frequency (VLF) component of heart rate variability (HRV). METHODS: Eight patients participated in this study. PA was measured using an accelerometer, and HRV was measured using a heart rate monitor. RESULTS: A significant and positive relationship was observed between the VLF component of HRV and PA. A significant negative relationship was observed between the VLF component of HRV and the duration of inactivity. No significant relationship was identified between the low-to-high frequency ratio of HRV and between the high-frequency component of HRV and PA. CONCLUSIONS: A positive correlation was observed between the VLF component of HRV and PA in stroke patients. Therefore, the VLF component of HRV links PA to cardiovascular prognosis.