Background The aim of this study was to investigate the effectiveness of acupuncture in decreasing the risk of stroke in patients with fibromyalgia. Methods We enrolled patients who was newly diagnosed as having fibromyalgia between 1 January, 2000 and 31 December, 2010 from the Taiwanese National Health Insurance Research Database. The claim data for both the acupuncture cohort and non-acupuncture cohort were assessed from the index date to 31 December, 2013. A Cox regression model adjusted for age, sex, comorbidities, and drugs use was used to compare the hazard ratios of the two cohorts. The cumulative incidence of stroke was estimated by using the Kaplan-Meier method. Results After performing a propensity score matching with a 1:1 ratio, there were 65,487 patients in the acupuncture and non-acupuncture cohorts with similar distributions in the baseline characteristics. The cumulative incidence of stroke was significantly lower in the acupuncture cohort (log-rank test, p < 0.001). In the follow-up period, 4,216 patients in the acupuncture cohort (11.01 per 1000 person-years) and 6,849 patients in the non-acupuncture cohort (19.82 per 1000 person-years) suffered from stroke (adjusted HR 0.53, 95% CI 0.51-0.55).