We report a case in which rabeprazole cured gastric tube ulcer after esophagectomy for esophageal squamous cell carcinoma (ESCC). A 47-year-old Japanese man was referred to our hospital with refractory ulcer of the reconstructed gastric tube one year after esophagectomy for ESCC. The ulcer proved refractory to healing by the administration of omeprazole or lansoprazole, or eradication of Helicobacter pylori after examinations concerning ischemia, acid over-secretion and H. pylori infection. Finally, metabolizer type was examined for proton pump inhibitors (PPIs), revealing the patient as a hetero-extensive metabolizer for the CYP2C19 genotype. This suggested sensitivity to rabeprazole, but resistance to omeprazole and lansoprazole. The refractory ulcer was subsequently cured after changing the PPI to rabeprazole. Examination of PPI metabolizer type might thus be important, along with an investigation of ischemia, acid secretion and H. pylori infection in the treatment of refractory gastric tube ulcer after esophagectomy.