Gastrointestinal stromal tumours (GIST) are tumours of gastrointestinal tract and mesentery. The commonest site of its occurrence is the stomach. Patients with GIST are usually asymptomatic but they can present as abdominal pain, bleeding and rarely gastric outlet obstruction. In this particular case, the patient presents with symptoms of anaemia, partial gastric outlet obstruction and intermittent epigastric pain. Laparotomy was performed and a diagnosis of gastroduodenal intussusception secondary to gastrointestinal stromal tumour was made.