BACKGROUND: Complex surgery during initial cancer treatment can limit surgical options when planning management of a secondary malignancy. Subtotal esophagectomy and pancreatoduodenectomy are the most invasive and difficult procedures in gastroenterological surgery. Surgical cases in which subtotal esophagectomy was performed after pancreatoduodenectomy with pancreaticogastrostomy are extremely rare and challenging procedures due to the resulting complicated anatomical changes. CASE PRESENTATION: A 60-year-old man with a history of conversion pancreatoduodenectomy with pancreaticogastrostomy for advanced pancreatic head cancer was diagnosed as having advanced thoracic esophageal squamous cell carcinoma. After neoadjuvant chemotherapy, we chose a two-staged surgery with thoracoscopic subtotal esophagectomy. Following percutaneous endoscopic gastrostomy, we performed subtotal esophagectomy, systematic lymph-node dissection, and esophagostomy as the first-stage operation. Fifty-six days later, we performed gastrointestinal reconstruction with pedicle jejunum and microvascular anastomosis by the percutaneous route as the second-stage operation. Postoperatively, the patient was relieved without major complications, and the tumors were amenable to curative pathologic resection. CONCLUSIONS: The greatest advantages of staged surgery are to reduce surgical invasiveness and to circumvent the lower rate of curability. Our procedure reported here may be recommended as an option for staged resection and reconstruction in patients with advanced esophageal cancer after pancreatoduodenectomy with pancreaticogastrostomy.