A man in his 30s visited our hospital after a local doctor diagnosed him with a rectal submucosal tumor. Colonoscopy and fine needle biopsy revealed a lower rectal gastrointestinal tumor (GIST). Pelvic MRI examination revealed apparent tumor invasion of the left levator ani muscle. Curative abdominoperineal resection( APR) of the tumor was required. Our strategy involved the initiation of neoadjuvant imatinib therapy to facilitate subsequent sphincter-preserving resection. Neoadjuvant chemotherapy for 11 months reduced the tumor size and permitted the R0 laparoscopic sphincter-preserving resection. He was discharged without any postoperative complications. The pathological findings revealed semi-curative effects and pR0 resection. Thus, neoadjuvant chemotherapy for advanced rectal GIST was a useful strategy for this function- preserving operation.