Abstract Background The detection rate of narrow-band imaging (NBI) for superficial esophageal squamous cell carcinoma (SESCC), including high-grade intraepithelial neoplasia, is significantly higher than that of white-light endoscopy. However, there are SESCCs that are undetectable by NBI but detectable by Lugol chromoendoscopy (LCE) and the characteristics of these SESCCs are still unknown. Thus, this study aimed to clarify the characteristics of SESCC that are undetectable using NBI. Methods Patients with current SCC or a history of SCC in the head and neck or in the esophagus were enrolled. The inspection of the esophagus was initiated by NBI, followed by LCE. Biopsies were taken of all suspected SESCC lesions during NBI observation and Lugol-voiding lesions (LVLs) that were irregularly shaped and >5 mm and/or pink in color during LCE observation. The characteristics of SESCC that were undetectable with NBI were statistically analysed. Results Overall, 147 lesions in 105 cases were histologically diagnosed as SESCC. Twenty in 15 cases were NBI-undetectable lesions, all of which were macroscopic flat type (0-IIb). The median sizes of the NBI-undetectable lesions and NBI-detectable lesions were both 15 mm (P = 0.47). Multivariate analysis revealed independent factors for NBI-undetectable lesions such as numerous irregularly shaped LVLs (odds ratio [OR]: 4.94, 95% confidence interval [CI]: 1.39–17.5, P < 0.05) and anterior wall position (OR: 4.99, 95% CI: 1.58–15.8, P < 0.05). Conclusions The detection of SESCCs with NBI is challenging when lesions are morphologically completely flat, in cases with numerous irregularly shaped LVLs, and if located at the anterior wall.