Background Foreign bodies that enter the pancreas and cause chronic complications cannot be removed by endoscopy. Surgical removal is necessary but also challenging. The development of augmented reality navigation has made it possible to accurate intraoperative navigation in laparoscopic surgery. Methods A 37-year-old female had epigastric pain for 3 months and her abdominal CT showed a linear high-density shadow in her pancreas along with chronic pancreatitis. Three-dimensional models of the liver, pancreas, stomach, blood vessels, and foreign body were created based on CT images. Gastroptosis was found in the three- dimensional models, so surgical approach was adapted to open the hepatogastric ligament to reach the pancreas. After 2-3 s of video images were captured by 3D laparoscopy, a three-dimensional dense stereo-reconstruction method was used to obtain the surface model of pancreas, stomach, and blood vessels. The Globally Optimal Iterative Closest Point method was used to obtain a spatial transformation matrix between the preoperative CT image space and the intraoperative laparoscopic space. Under augmented reality navigation guidance, the position and location of the foreign body were displayed on the surface of the pancreas. Then intraoperative ultrasound was used for further verification and to quickly and easily confirm the surgical entrance. After minimal dissection and removal of the pancreatic parenchyma, the foreign body was removed completely. Results The operation time was 60 min, the estimated blood loss was 10 ml. The foreign body was identified as a 3-cm-long fishbone. The patient recovered without complications and was discharged on the third postoperative day. Conclusion Because it enables direct visual navigation via simple operation, ARN facilitates the laparoscopic removal of foreign bodies in the pancreas with accurate and rapid positioning and minimal damage.