Studies have indicated that serum pepsinogen (PG) levels are not only markers for chronic atrophic gastritis but also predictive risk factors for gastric cancer. However, serum PG levels can change because of pathological conditions other than gastritis. We report the first case in which abnormally high serum PG II levels (168.8 ng/mL) led to the discovery of a large tumor covering a wide area in the duodenum, and after resection of the tumor, the serum PG II levels markedly decreased. Because endoscopic and histopathological examinations showed no indications of atrophic changes, inflammation of the gastric mucosa, or Helicobacter pylori infection, the serum PG II levels eventually returned to normal (10.1 ng/mL). The preoperative abnormally high PG II levels were probably caused by the large duodenal tumor that prevented PG II (which is produced by the duodenal Brunner's glands) from being secreted into the lumen, a condition that increased the amount transferred to the bloodstream. No previous reports have investigated serum PG II levels before and after resection of a large duodenal tumor. We believe this case provides valuable insight regarding the dynamics of PG II in the body and has important diagnostic implications.