Gastrointestinal stromal tumours (GISTs) are generally rare but are known to be the most common mesenchymal tumours of the gastrointestinal tract. We present a case of a patient who presented with persistent obstructive gastrointestinal and urological symptoms, a sense of incomplete evacuation and bleeding per rectum. A colonoscopy was performed and a biopsy was taken of a submucosal mass in the distal rectum that revealed a GIST with positive KIT immunostaining. A positron emission tomography (PET)/CT scan showed a large metabolically active distal rectal tumour of 8 cm with macroscopic invasion of surrounding structures. Neoadjuvant therapy with receptor tyrosine kinase inhibitor imatinib (400 mg orally daily) was initiated and an excellent partial response consisting of a significant decrease in the size of the tumour with complete metabolic resolution was observed within 3 months. Six months after initiation of the neoadjuvant therapy a rectum resection with manual side-to-end coloanal anastomosis was performed. Pathology showed a GIST of 5 cm located 0.1 cm from the distal section plane. Our case shows that in patients with a large invasive distal rectal GIST, neoadjuvant imatinib therapy can facilitate anal sphincter sparing surgery.