Parkinson’s disease (PD) is associated with a significantly increased risk of stroke. Traditional Chinese medicine (TCM) has long been used in Asia to treat stroke, but there are no large-scale clinical data to confirm its efficacy in protecting PD patients against stroke. Herein, we analyzed a cohort of 1,000,000 records from Taiwan’s National Health Insurance Research Database for the period 1997–2011, and identified 1,882 patients with new-onset PD. We matched 290 patients who received Chinese herbal medicine (CHM) by age, sex, year of CHM prescription, and year of PD diagnosis with 290 patients who did not use CHM as control. Both cohorts were followed until the end of 2013 for the incidence of new-onset stroke. In a multivariable Cox proportional hazard model adjusted for potential comorbidities, the incidence of stroke was lower among PD patients using CHM compared with non-CHM users (11.10 per 100 person-years vs 23.15 per 100 person-years; Hazard ratio: 0.56; 95% confidence interval:  0.44 to 0.72). The probability curve generated from our follow-up data showed that PD patients receiving CHM treatment had a decreased risk of stroke compared with those not receiving CHM treatment (P <0.001). The analysis on the prescription pattern of CHM revealed that Danshen is the most common single herb and Ma Zi Ren Wan is the most common herbal formula. Although the analysis are limited by a lack of analytic information regarding lifestyle patterns, biochemical profiles, and levels of PD severity in database, this population-based study suggest that CHM may be an complementary therapy to reduce the risk of stroke in PD patients.