Background: Eosinophilic esophagitis (EoE) and gastroesophageal reflux disease (GERD) are distinct conditions, yet they often exhibit overlapping clinical, endoscopic, and histological features. Aim: This study aims to assess the prevalence of GERD among patients with EoE and to identify risk factors for both typical and atypical GERD symptoms. Methods: We conducted a population-based retrospective analysis of patients diagnosed with EoE and collected data on demographics, GERD diagnosis, symptoms, comorbidities, and laboratory results. GERD symptoms were classified as typical (e.g., heartburn and regurgitaion) or atypical (e.g., hoarseness and cough). Results: Of the 2,496 patients with EoE (73.2% male), 48.5% exhibited GERD symptoms—26.2% prior to and 30.5% following the diagnosis of EoE. Typical symptoms predominated before EoE diagnosis (26% vs. 4.3% after diagnosis), whereas atypical symptoms were more frequent after diagnosis (28% vs. 0.4% before diagnosis), with cough increasing from 0.4% to 27.4%. In the multivariate analysis, allergic rhinitis (odds ratio [OR 1.40, 95% confidence interval [CI]; 1.15–1.75, p < 0.001) and hiatal hernia (OR 2.47, 95% CI 1.75–3.47, p < 0.001) predicted typical GERD symptoms, whereas asthma (OR 1.50, 95% CI 1.28–1.85), food allergy (OR 1.36, 95% CI 1.08–1.70), and elevated eosinophil counts (OR 2.00, 95% CI 1.44–2.73) were associated with atypical GERD symptoms. Conclusion: Approximately half of patients with EoE are present with GERD symptoms, with a tendency toward more atypical symptoms after EoE diagnosis. Identifying key predictors and risk factors may improve diagnostic accuracy and facilitate the development of targeted treatment strategies.