Objectives Functional abdominal pain disorder (FAPD) is common in children and adults. However, the mechanism of FAPD is not clearly known. Recently, micro-inflammation, especially eosinophilia in the gastrointestinal tract, was suggested in the pathophysiology of FAPD in adults. The aim of this study was to evaluate eosinophil infiltration in the entire gastrointestinal tract in children with FAPD, compared to those with inflammatory bowel disease (IBD). Methods In total, 56 pediatric patients with FAPD, 52 children with Crohn’s disease (CD), and 23 children with ulcerative colitis (UC) were recruited. All subjects underwent esophagogastroduodenoscopy, colonoscopy, and endoscopic biopsies in the same day. Tissue eosinophil counts were assessed in 10 regions of the entire gastrointestinal tract from the stomach to the rectum. Tissue eosinophil counts were compared between FAPD and IBD. To minimize effects of IBD itself inflammation, after eliminating pathology slides of local parts confirmed as severe inflammation by endoscopy exam, eosinophil counts were analyzed as well. Tissue eosinophil counts of FAPD patients were also compared to those from normal pathology references. Results Before excluding local anatomic regions with active inflammation of IBD, analysis between FAPD and IBD revealed that the stomach and the entire colon tract of pediatric IBD patients had significantly higher eosinophils than those with FAPD. Eosinophil counts of the duodenum and the terminal ileum were also higher in children with IBD, but not significantly when compared with FAPD. Even after deducting biopsy slides from active mucosal lesions, IBD patients showed significantly higher tissue eosinophils in the gastric body, cecum, descending colon, sigmoid colon, and rectum than those with FAPD. Children with FAPD patients showed significantly higher eosinophil counts in the gastric antrum, duodenum, terminal ileum, cecum, and ascending colon than normal reference values. Conclusion The present study reveals tissue eosinophils infiltration is related to gastrointestinal inflammation. Particularly, eosinophils infiltration in the stomach and the colon seem to be more associated with intrinsic pathogenesis of both FAPD and IBD, regardless of local inflammation. This suggests some contribution of gastrointestinal eosinophils in the development of pediatric IBD as well as FAPD.