Recurrent stroke increases mortality and aggravates the disability of stroke patients. We hypothesized that increased inter-arm systolic blood pressure difference and inter-arm diastolic blood pressure difference would be related to recurrent stroke in non-cardioembolic stroke patients. A total of 1226 consecutive non-cardioembolic first-ever ischemic stroke patients, in whom bilateral brachial blood pressures were measured by an automated ankle-brachial index measuring device, were included in our study. Recurrent stroke was defined as newly developed neurologic symptoms with relevant lesions on brain CT and/or MRI after 7 days or hospital discharge. Inter-arm systolic and diastolic blood pressure differences ≥10 mmHg were noted in 9.7% (120/1226) and 5.0% (62/1226) of patients, respectively. During a median 24 months of follow-up, 105 (8.5%) patients experienced recurrent stroke. Patients who had inter-arm systolic blood pressure difference ≥10 mmHg showed increased risk of recurrent stroke (hazard ratio:1.77, 95% confidence interval: 1.04–3.00, p = 0.033). Moreover, inter-arm diastolic blood pressure difference ≥10 mmHg was also independently associated with increased risk of recurrent stroke (hazard ratio:2.92, 95% confidence interval: 1.59–5.34, p = 0.001). In conclusion, inter-arm blood pressure difference ≥10 mmHg may be associated with increased risk recurrent stroke in non-cardioembolic stroke patients.