Non-erosive reflux disease (NERD) is a highly prevalent phenotype of the gastroesophageal reflux disease (GERD). In this study, we developed a novel murine model of NERD in mice with microscopic inflammation and impairment in the epithelial esophageal barrier. Female Swiss mice were subjected to the following surgical procedure: the transitional region between the forestomach and the glandular portion of the stomach was ligated, and a nontoxic ring was placed around the duodenum near the pylorus. The control group underwent sham surgery. The animals were sacrificed at 1, 3, 7, and 14 days post-surgery. Survival and body weight were monitored daily. Esophageal wet weight, macroscopic lesion, histopathological alterations, myeloperoxidase (MPO) activity, cytokines levels, transepithelial electrical resistance (TEER), and mucosal permeability were evaluated. The survival rate was 78% at 14 days, with mild loss in body weight. Surgery did not induce erosive esophagitis, but instead induced microscopic inflammation, increased esophageal wet weight, IL-6 and keratinocyte-derived cytokine (KC) levels, and MPO activity with maximal peak between 3 and 7 days, and resolution at 14 days post-surgery. Epithelial esophageal barrier was evaluated in operated mice at 7 and 14 days post-surgery; decrease in TEER and increase in the esophageal epithelial permeability were observed, compared to sham group. In addition, the inhibition of acid secretion with omeprazole significantly prevented the esophageal inflammation and impairment of barrier function at 7 days post surgery. Thus, we established a novel experimental model of NERD in mice, which can contribute to understanding the pathophysiological events associated with NERD.