Duodenal gastrointestinal stromal tumours (D-GISTs) are rare disease. It may arise commonly from second or third part of the duodenum and can be erroneously diagnosed as a pancreatic head tumour due to proximity and morphology on imaging studies. We present a case of a sixty-year-old woman who presented with abdominal pain and was diagnosed as a case of pancreatic neuroendocrine tumour on radiologic imaging and granulomatous lesion on aspiration cytology. On laparotomy, a ~5x3 cm mass was noted in the pancreatic head and pancreatoduodenectomy was performed. Histopathology reported an exophytic GIST arising from the second part of the duodenum.Hence, D-GIST can invade into the pancreas and mimic pancreatic head tumour; therefore, these tumours should be kept in the differential diagnosis of an atypical pancreatic head mass.