A 72-year-old man was diagnosed with tumors outside of the stomach and mesentery of the small intestine on abdominal computed tomography. Histopathological examination of an endoscopic ultrasound-guided fine-needle aspiration biopsy specimen confirmed the diagnosis of lymph node metastasis of a neuroendocrine tumor (NET). Gastroscopy, colonoscopy, small bowel capsule endoscopy, somatostatin receptor scintigraphy, and 18F-fluorodeoxyglucose positron emission tomography were performed. However, the primary lesion could not be diagnosed. The patient underwent surgery, and an ileal submucosal tumor, which was not identified preoperatively in addition to the aforementioned abdominal tumors, was detected. All tumors were diagnosed as NET, and the ileal tumor was considered the primary lesion. The patient has shown no recurrence postoperatively. The current study presents a case of an ileal NET with lymph node metastases in a patient in whom the primary lesion remained preoperatively undiagnosed.