Objective: We recently measured the longitudinal use of secondary prevention medication following hospital discharge and the factors influencing persistence in patients with acute ischemic stroke (AIS) and transient ischemic attack (TIA) in China. Methods: Patients with AIS and TIA who were enrolled in the China National Stroke Registry II from June 2012 to January 2013 were surveyed to determine persistence. The medications included antiplatelet therapies, warfarin, antihypertensive therapies, statins, and diabetes medications. We determined persistence for a three-month period following discharge. Persistence was defined as the continuation of all secondary preventive medications prescribed upon hospital discharge. The factors associated with medication persistence 3 months after discharge were examined using a multivariable logistic regression. Results: Of the 21,592 patients with AIS and TIA, 18,344 (91.2%) were eligible for analysis. After 3 months post-discharge, 46.2% of the subjects continued to take all secondary prevention medications prescribed at discharge. Independent predictors of three-month medication persistence included younger age, absence of a history of diabetes or atrial fibrillation, higher family income, less severe stroke, index cerebrovascular event of ischemic stroke, and being treated in a hospital with a stroke unit and more beds in the neurology department. Conclusions: More than half of patients with AIS and TIA reported discontinuing one or more secondary prevention medications within 3 months of hospital discharge. Several factors associated with medication persistence were identified. Here, we propose strategies that could be implemented to improve the quality of secondary prevention.