Gastrointestinal stromal tumor (GIST) is the most common mesenchymal neoplasm of the gastrointestinal tract. However, rectal GIST is rare, the incident rate of it is approximately 5% of all GISTs. Rectal GIST symptoms generally include bleeding and/or pain and occasionally, urinary symptoms. Immunohistochemical evaluation finds that most rectal GIST tumors are CD117 (KIT) positive, and are sometimes CD34, platelet-derived growth factor receptor alpha (PDGFRA), smooth muscle actin, S-100, or vimentin positive. The National Institutes of Health (NIH) classifies rectal GIST as very-low risk, low risk, intermediate risk, or high risk, and the frequencies have been estimated as 0-23.8% for very-low risk, 0-45% for low risk, 0-34% for intermediate risk, and 21-100% for high risk tumors. The first-line treatment for localized GIST is curative resection, but is difficult in rectal GIST because of anatomical characteristics such as the deep, narrow pelvis and proximity to the sphincter muscle or other organs. Several studies noted the efficacy of the minimally invasive surgery, such as trans-anal, trans-sacral, trans-vaginal resection, or laparoscopic resection. The appropriate surgical procedure should be selected depending on the case. Imatinib mesylate (IM) is indicated as first-line treatment of metastatic or unresectable GIST, and clinical outcomes are correlated with mutation genotype. However, the mutation genotypes in rectal GIST are not well known. In this review, as in other GISTs, a large proportion (59-100%) of rectal GISTs carry exon 11 mutations. Although curative resection is indicated for localized rectal GIST, a high rate of local recurrence is a problem. Multimodal therapy including perioperative IM may improve postoperative outcomes, contributing to anus-preserving surgery. Moreover, mutation analysis before IM treatment is important. This review summarizes current treatment strategies for rectal GIST.