Background Food protein-induced enterocolitis syndrome (FPIES) is a non-immunoglobulin E (IgE)-mediated food allergy that affects infants. It is characterized by massive and repetitive vomiting, lethargy, pallor, and watery diarrhea. Although FPIES can mimic acute gastrointestinal diseases, for which ultrasonography is useful, few studies on ultrasonographic findings in non-IgE-mediated food allergic disorders are available. We investigated the ultrasonographic features of patients with FPIES. Methods Patients who underwent an oral food challenge (OFC) test or were diagnosed with acute FPIES were enrolled. We divided the patients into the FPIES and non-FPIES groups. Ultrasonography was performed before and 6h after the OFC test. Patients in the FPIES group underwent ultrasonography 24 h after the OFC tests. We evaluated intestinal findings, including peristaltic movement, fluid accumulation, and wall thickness of the gastrointestinal tract. Results Fourteen patients in the FPIES group and 11 in the non-FPIES group were enrolled. Ultrasonography performed 6h after the OFC test showed that the number of patients with small intestinal fluid accumulation and hyperperistalsis was significantly higher in the FPIES group than in the non-FPIES group. In the FPIES group, jejunal wall thickness significantly increased 6h after the OFC test. Small bowel intussusception occurred in three patients with FPIES. Conclusions Small-intestinal wall thickening, fluid accumulation, and abnormal peristalsis on ultrasonography suggest its utility in diagnosing FPIES. In cases of small intestinal intussusception, FPIES should be considered in the differential diagnosis.