Functional abdominal pain disorders (FAPDs) are among the most common types of chronic pain disorders in children. FAPD symptoms are characterized by chronic abdominal pain and changed bowel movements. The pathophysiology of FAPDs in children is unknown, but these conditions may have an imprecise clinical overlap to food intolerance/malabsorption. We report on 51 consecutive children (23/28 males/females; median age 15.3 years) with investigated FAPDs from 2017 to 2022 in this retrospective pilot study. Small intestinal biopsies in children demonstrated the association of lactase and diamine oxidase (DAO), which prompted us to perform hydrogen (H2) breath tests for lactose intolerance (LIT) and determine serum DAO for the evaluation of histamine intolerance (HIT) in pediatric patients with FAPDs. To complete the food intolerance/malabsorption evaluation tests, we included a search for antibodies against tissue transglutaminase to find celiac disease (CD), performed H2 breath tests to detect fructose malabsorption (FM), and conducted a search for IgA antibodies against H. pylori infection. The results demonstrate that all 51 children evaluated were diagnosed with food intolerance/malabsorption and/or various combinations thereof. Seven children showed FM, eight of the children had HIT, and eight children had LIT. The other children had combinations: thirteen children (25.5%) had HIT and LIT, seven children (9.8%) had FM with HIT, five children (13.7%) had FM and LIT, and three children (5.9%) had a triple combination of FM, HIT, and LIT. By describing this method of personalized investigation for food intolerance/malabsorption in children with FAPDs, we demonstrate that functional abdominal pain disorders may be associated with food intolerance/malabsorption. After such diagnosis in this pediatric population, a registered dietitian helped to establish a reduction and/or exclusion diet individually tailored to their symptomatology.