<b><i>Background/Aim:</i></b> The aim of this study was to compare the accuracy of magnifying endoscopy with narrow band imaging for the diagnosis of depth of invasion by Japan Esophageal Society (JES) classification and inter- and intraobserver agreement of JES intrapapillary capillary loop (IPCL) classification. <b><i>Methods:</i></b> It was a retrospective observational study that has analyzed 136 patients with esophageal malignant neoplasia with magnifying endoscopy narrow band imaging to compare JES’s IPCL classification to the histopathologic findings and to evaluate the inter- and intraobserver agreement. <b><i>Results:</i></b> Histopathologic examinations revealed 34 (25.7%) intraepithelial neoplasias, 70 (51.5%) squamous cell carcinomas (SCCs) in the epithelium or with invasion into the lamina propria mucosa, 21 (15.4%) SCCs with invasion into the muscularis mucosa or mild invasion into the submucosa, and 11 (8.1%) SCCs with moderate or deep invasion into the submucosa. IPCL types B1, B2, and B3 also showed high accuracies of 80.8, 83.1, and 94.1%, respectively. The kappa values for inter- and intraobserver agreements of the IPCL classifications were moderate to almost perfect. <b><i>Conclusions:</i></b> In the present study, the JES’s IPCL classification has good accuracy to predict the depth of SCC invasion and moderate to almost perfect intra- and interobserver agreements.