Congenital esophageal web is a very rare type of esophageal atresia (EA) and is considered as Type IV atresia in Kluth's classification. Type IV EA is further classified into subgroups according to the location of web and the presence of tracheoesophageal fistula (TEF). Herein, we present a newborn having Type IV1a EA who was initially suspected as isolated EA and has co-existing malrotation together with the review of the literature. A newborn having congenital esophageal web was admitted with antenatal ultrasonography revealing polyhydramnios, dilated stomach, and duodenum. Abdominal X-ray revealed a gasless abdomen suggesting isolated EA. The upper gastrointestinal series confirmed complete obstruction at the lower esophagus. Bronchoscopy performed excluding TEF. Laparotomy revealed intestinal malrotation and the absence of another GI webs. Gastrotomy was performed and mucosal web at GEJ was seen by pushing nasogastric catheter. Web excision and Ladd procedure were performed. Congenital esophageal web is an extremely rare type of esophageal anomaly that can be only classified in Kluth classification. A high index of suspicion is required for diagnosis especially in newborns with the gasless abdomen and esophageal obstruction at the level of GEJ. Preoperative bronchoscopy is mandatory to exclude an associating TEF. Surgical exploration via laparotomy is beneficial for exploring additional GIS anomalies.