Although intussusception and food allergy are common health problems in childhood, the relation between these two diseases remain obscure. The aim of this study is to investigate the relationship between food allergy and intussusception, and the factors associated with both. Patients diagnosed with intussusception by the Brighton Collaboration Intussusception Working Group criteria were prospectively investigated for food allergy per the European Society for Pediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) Guideline. They were analyzed per demographic features, clinical, physical and laboratory findings. There were eight (38.1%) patients diagnosed with food allergy, while 13 (61.9%) patients were non-allergic. The mean number of days of presenting symptoms was 1.13 days in the allergy group and 7.85 days in the non-allergy group. The mean number of intussusception attacks was 1.63 in the allergy group while 1 in the non-allergy group (p < 0.05, relative risk (RR) = 2.6). In the allergy group, one (13%) patient was followed up, six (75%) patients were reduced with pneumatic and one (13%) patient reduced manually. In the non-allergy group, four (31%) patients were followed up, six (46%) patients were reduced with pneumotic, one (7%) patient was reduced manually, and resection anastomosis was performed in two (15%) patients. Food allergy is an unrecognized associated factor for intussusception patients, which increases the risk for recurrence. Due to the small patient population, these results should be interpreted with caution.