A multimodal treatment has been applied for patients with rectal gastrointestinal stromal tumor (GIST) that represents 5% of the total localization. Meanwhile, transanal endoscopic microsurgery (TEM) offers a minimally invasive method for full-thickness tumor excision with negative margins and low morbidity. We report the single most extensive analysis of data from China to evaluate the feasibility and safety of the procedure combined with neoadjuvant imatinib therapy to treat patients with rectal GISTs. All the clinical data were obtained for patients who underwent the procedure in our hospital from February 2008 to May 2015, and the data were retrospectively analyzed. Full-thickness excision by TEM was performed on 25 patients with rectal GIST by using primary surgical excision, 8 of whom had received perioperative chemotherapy after histopathological confirmation under the care of medical oncologists. No obvious postoperative complications were observed. The average tumor downsizing ratio was 14.5%, which apparently enabled oversized tumors to be resected by TEM. The comparative risk did not increase during or after the procedure. We did not observe recurrence or metastasis in any of the 25 patients during the median 3-year follow-up period after the procedures. The perioperative imatinib treatment effectively allowed oversized rectal GIST tumors to be resected by TEM, and the procedures did not exhibit an increased risk. Exclusively, the TEM procedure with alternative neoadjuvant imatinib therapy is a feasible and safe modality for treating patients with rectal GISTs.