A 20-year-old woman presented to our hospital with abdominal pain. Abdominal computed tomography revealed multiple masses in the upper jejunum, which were suspected as lipomas. Partial resection of the small intestine, including the masses, was performed on the same day due to intussusception secondary to the masses. Pathological examination revealed that the masses consisted of mucosa and edematous submucosa with multiple dilated blood vessels and lymphatic ducts without muscularis propria. The masses were diagnosed as multiple muco-submucosal elongated polyps (MSEP), a type of non-neoplastic polyp. MSEP was originally named colonic MSEP, but with the development of endoscopic techniques and imaging tests, similar polyps have been reported to occur not only in the colon but also in the entire intestinal tract. In this case, multiple MSEPs in the upper jejunum caused intussusception. As reported cases of multiple lesions causing intussusception are few, our case may help to clarify the pathogenesis of this disease.