With the advancement of imaging and pathological diagnostic methods, it is not uncommon to see synchronous gastrointestinal stromal tumors (GIST) and other primary cancers, the most common of which are synchronous gastric cancer and gastric GIST. However, synchronous advanced rectal cancer and high-risk GIST in the terminal ileum are extremely rare, and they are easily misdiagnosed as rectal cancer with pelvic metastases due to their special location near iliac vessels. Herein, we report a 55-year-old Chinese woman with rectal cancer. Preoperative imaging revealed a middle and lower rectal lesion with a right pelvic mass (considered possible metastasis from rectal cancer). Through multidisciplinary discussions, we suspected the possibility of rectal cancer synchronous with a GIST in the terminal ileum. Intraoperative exploration by laparoscopy revealed a terminal ileal mass with pelvic adhesion, a rectal mass with plasma membrane depression, and no abdominal or liver metastases. Laparoscopic radical proctectomy (DIXON) plus partial small bowel resection plus prophylactic loop ileostomy was performed, and the pathological report confirmed the coexistence of advanced rectal cancer and a high-risk ileal GIST. The patient was treated with the chemotherapy (CAPEOX regimen) plus targeted therapy(imatinib) after surgery, and no abnormalities were observed on the follow-up examination. Synchronous rectal cancer and ileal GIST are rare and easily misdiagnosed as a rectal cancer with pelvic metastases, and careful preoperative imaging analysis and prompt laparoscopic exploration are required to determine the diagnosis and prolong patient survival.