Background <p>Membranous esophageal atresia (MEA) without tracheoesophageal fistula (TEF) is a rare form of esophageal atresia (EA) that is often misdiagnosed as Gross type A esophageal atresia (isolated EA). However, the management strategies for these two conditions differ substantially. We present a case initially diagnosed as Gross type A EA, in which intraoperative recognition of key findings led to a revised diagnosis of MEA without TEF, enabling a single-stage repair and avoiding unnecessary staged reconstruction. Additionally, we have reviewed the literature to summarize the clinical characteristics and diagnostic clues to facilitate timely and accurate diagnosis.</p> Case presentation <p>A female neonate presented with classic signs of EA. Preoperative imaging revealed esophageal obstruction with a relatively long proximal pouch and a gasless abdomen, suggesting Gross type A EA. Intraoperative retrograde esophagography revealed a short gap between the proximal and distal pouches, and thoracoscopic exploration identified preserved external esophageal continuity with obstruction caused by an intraluminal membrane. The membrane was resected, and a primary anastomosis was performed under thoracoscopy. The patient recovered uneventfully and was asymptomatic at the two-year follow-up.</p> Conclusions <p>MEA without TEF can mimic Gross type A EA. Key features for this condition include a relatively distal proximal pouch, a short gap between the proximal and distal esophageal pouch, and intraoperative visualization of preserved esophageal continuity. Clinicians should maintain a high index of suspicion for this rare variant to guide appropriate surgical management when a newborn with EA presents these features. Thoracoscopic surgery represents a safe and effective approach for this condition.</p>