Introduction: Clopidogrel resistance causes recurrent stroke. However, outcomes of modified antiplatelet medications to prevent recurrent ischemic stroke are not well known. Methods: Patients who received clopidogrel with and without modification as initial treatment for stroke were recruited and compared. The primary outcome was ischemic stroke and myocardial infarction at the 1-year follow-up. The secondary outcome was bleeding complications. Results: Overall, 206 patients treated with clopidogrel were enrolled and were divided into the modification (n = 39) and no modification (n = 167) groups. There was a significant difference in the incidence of severe cerebral arterial stenosis between the two groups (modification group, 16/39, 41.03%; no modification group, 36/167, 21.56%, P = 0.012) at baseline. The loss to follow-up rate was 12.14% (25/206). After adjustment for severe cerebral artery stenosis, antiplatelet modification based on the platelet reactivity unit (PRU) value significantly improved in the per protocol set (odds ratio 0.142, 95% confidential interval 0.022-0.898, P = 0.038). The area under the curve of the different PRU cutoff values were 0.630, 0.605, and 0.591 (P = 0.016, 0.051, and 0.092) for PRU 190, 208, and 235, respectively. Conclusion: Verifynow P2Y 12 PRU-guided modification of clopidogrel for ischemic stroke significantly improved or prevented recurrence at the 1-year follow-up. Our findings suggest that clopidogrel therapy based on the PRU cutoff value of 190 should be considered to improve outcomes. Trial Registration: ClinicalTrials.gov NCT02618265 (December 1, 2015).