Background/Objectives: There is a limited body of evidence regarding dietary intake in children with inflammatory bowel disease despite increasing research about the nutritional implications in the disease pathogenesis. Functional abdominal pain disorders (FAPDs) are also chronic disorders marked by chronic abdominal pain, currently described with the ROME IV criteria. This study was aimed to investigate the adherence to healthy eating habits in an inflammatory bowel disease pediatric population when compared to a matched population with functional abdominal pain gastrointestinal disorders. Methods: We performed a single centre study focused on dietary patterns in children with IBD and FAPDs between January 2021 and April 2024. Data collected included general information, disease phenotype, and the KIDMED index regarding healthy eating. Results: The final analysis was based on full data from the KIDMED index available for 122 (57 vs. 65) participants. Overall, the average KIDMED score did not vary significantly between the study population, meaning 6.89 +/- 2.33 for the IBD group and 7.11 +/- 2.67 for FAPDs group, p = 0.34. In the same KIDMED index group, mean values were higher for FAPDs patients, but results differ statistically significant only for "medium" adherence to healthy diet, showing that larger proportion of IBD patients were previously exposed to non-healthy diets: 8.99 vs. 11.1, p = 0.45, 5.02 vs. 6.92, p = 0.05, 2.89 vs. 2.56, p = 0.43, for group 1, 2, and 3, respectively. Conclusions: This study showed in our cohort that overall adherence to a healthy pattern diet is poor prior to diagnosis of different gastrointestinal pathologies in children.