This study applied a counterpulsation (CP) control method based on a phase-locked loop (PLL) algorithm to synchronise a pneumatic pulsatile ventricular assist device (VAD) with the hearts of patients with arrhythmias. Electrocardiogram data obtained from 40 patients with arrhythmias were used as the input signal for the pulsatile VAD, and the effects of the arrhythmia and the CP control of the VAD on the patients’ haemodynamic states were evaluated. The CP failure rate increased when tachycardia occurred; however, 85 % of the VAD pulses did not occur during heart contraction within 0.1 seconds of the QRS wave. When co-pulsation between the VAD and heart occurred, the aortic pressure did not exceed 140 mmHg and the load on the ventricles remained constant. The PLL CP control algorithm used in this study was able to maintain the CP continuously without increasing the heart load, even when arrhythmias occurred.