This study evaluated the effect of different frequencies in treating motor dysfunction of ischaemic stroke patients with electrical acupoint stimulation (EAS). Sixty-two ischaemic stroke patients with motor dysfunction were enrolled. Participants had been hospitalised after 1 week to 1 month from onset. They were treated with 2 Hz or 120 Hz EAS for 2 weeks, and had motor evoked potentials (MEPs) tests before and after. Latency, central motor conduction time (CMCT) and amplitude of MEPs were measured. After 2 weeks of treatment, MEPs data of the affected side between the 2 Hz group and the 120 Hz group was compared. The 2 Hz group showed more significant improvement than the 120 Hz group in latency, CMCT and amplitude. In the case of the affected side, MEPs data divided by normal side MEPs data, the 2 Hz group also showed higher improvement rate than the 120 Hz group in latency, CMCT and amplitude with significant differences.