Introduction Eosinophilic esophagitis (EoE) is not a common differential diagnosis in patients with longstanding refractory gastroesophageal reflux disease (GERD). The aim of this retrospective analysis was to assess the prevalence of EoE in patients with refractory GERD. Methods This retrospective analysis was performed in the Gastroenterology Department of a tertiary care institute in Karachi, Pakistan. Records of esophagogastroduodenoscopy (EGD) with esophageal biopsy from January 2016 till December 2018 were included. Results There were 16 (7.7%) patients of refractory GERD diagnosed with EoE. There were more females than males (5:3). The median age was 58 years (range: 41-63 years). Dysphagia was the chief complaint leading to EGD followed by food impaction and heartburn. The median duration of symptoms was 46.5 months (range: 22-65 months). Erosive esophagitis, white plaques, and friability are common endoscopic findings; however, strictures are also not uncommon. Conclusion Eosinophilic esophagitis is not uncommon in patients with refractory GERD. It may present with dysphagia, heartburn, and food impaction. Old patients with longstanding GERD, positive for atopy, not responding to gastric acid inhibitors must be considered for EoE screening via EGD and esophageal biopsy.