The aim of this study was to investigate the effect of influenza vaccination (and annual revaccination) on the risk of stroke admissions. We conducted a population-based case-control study in Taiwan. Cases consisted of patients >65 years of age who had a first-time diagnosis of stroke during the influenza seasons from 2006 to 2009. Controls were selected by matching age, sex, and index date to cases. Multiple logistic regression analysis was used to calculate the adjusted odds ratios (ORs) and 95% confidence intervals (CIs). Ever vaccinated individuals in the current vaccination season were associated with a reduced risk of ischemic stroke admissions (OR = 0.76, 95% CI = 0.60–0.97). Compared with individuals never vaccinated against influenza during the past 5 years, the adjusted ORs were 0.92 (95% CI = 0.68–1.23) for the group with 1 or 2 vaccinations, 0.73 (95% CI = 0.54–1.00) for the group with 3 or 4 vaccinations, and 0.56 (95% CI = 0.38–0.83) for the group with 5 vaccinations. There was a significant trend of decreasing risk of ischemic stroke admissions with an increasing number of vaccinations. This study provides evidence that vaccination against influenza may reduce the risk of hospitalization for ischemic stroke and that annual revaccination provides greater protection.