Gastrointestinal stromal tumors (GIST) are mesenchymal spindle cell tumors of the gastrointestinal tract with the rarest occurrence in anal canal sites accounting for approximately only 2-8% of the anorectal GISTs. GISTs involve the expression of KIT (CD117) tyrosine kinase with the presence of mutations in KIT or platelet-derived growth factor alpha (PDGFRα) and are identified as an important target in therapy. The elderly population in the age of 70s appears to be at the highest risk with abdominal pain, GI bleeding, anemia, or weight loss as non-specific presenting symptoms. Here, we describe a case of a 56-year-old man who presented with vague dull pain in his left buttock diagnosed with GIST with a submucosal mass in the posterior wall of the anal canal and rectum and a tumor size of 45x42x37 mm. An immunohistological study of the biopsy sample reported positive for CD 117, CD 34, and DOG 1. The patient was prescribed neoadjuvant imatinib for 8 months with a good response and subsequently underwent transanal endoscopic microsurgical resection. Post-operatively, the patient was continued on adjuvant imatinib followed by regular restaging CT chest/abdomen/pelvis and surveillance flexible sigmoidoscopy every 6 months.