Gastrointestinal stromal tumors or “GIST” are mesenchymal neoplasms expressing KIT(CD117) tyrosine kinase and showing the presence of activating mutations in KIT or PDGFRα (platelet–derived growth factor alpha). GIST of anal canal is an extremely rare tumor, accounting for only 3% of all anorectal mesenchymal tumors and 0.1–0.4% of all GIST. GIST with large tumor size and high mitotic activity are highly malignant, but the biological behavior of anorectal GIST is less clear. Abdominoperineal resection (APR) or conservative surgery is the best treatment option. Imatinib mesylate, a tyrosine kinase inhibitor, has shown promising results in its management. We present a case of rectal GIST which presented as irreducible rectal prolapse.The patient underwent abdominoperineal resection (APR) and was confirmed on histopathology to have rectal GIST with tumor size more than 5 cm in maximum dimension