Fibromyalgia (FM) tends to coexist with gastroesophageal reflux disease (GERD). This retrospective cohort study was conducted to determine the bidirectional association between FM and GERD, using a nationwide database, the National Health Insurance of Taiwan. We established 2 study arms, including 35,117 patients with FM in arm 1 and 34,630 patients with GERD in arm 2, newly diagnosed between 2000 and 2010. For each study arm, we randomly selected 4-fold subjects with neither FM nor GERD from the same database, frequency matched by sex, age, and diagnosis date, as the respective control cohorts. Incidence of GERD in arm 1 and incidence of FM in arm 2 were estimated by the end of 2011. The overall incidence of GERD was 1.6-fold greater in the FM cohort than in the non-FM cohort (12.0 and 7.61 per 1000 person-years, crude hazard ratio [HR] = 1.58, 95% confidence interval [CI] = 1.51-1.66), with an adjusted HR (aHR) of 1.27 (95% CI = 1.22-1.33) after controlling for sex, age, comorbidities, and medications. The GERD cohort ultimately had a 1.5-fold higher incidence of FM than the non-GERD cohort (5.76 vs 3.96 per 1000 person-years), with an aHR of 1.44 (95% CI = 1.29-1.60). The present study suggests a bidirectional relationship between FM and GERD. There is a greater risk of developing GERD for patients with FM than developing FM for patients with GERD.