Background: Functional gastrointestinal diseases (FGIDs) are an important yet highly under explored area among public health issues. FGIDs’ complex etiology makes them of interest along with their prevalence in children steadily increasing, especially in the developing world. We aimed to determine the burden FGIDs pose on school-going children, and to determine its association with the dietary intake patterns in Pakistani children. Methodology: The study included 385 school-children from public and private schools in Pakistan through multistage random sampling, from March to August 2022. We used the Food Frequency Questionnaire (FFQ) and Rome IV Criteria for a comprehensive exploration of the issue. Associations between the FGIDs and dietary factors were analyzed using chi-square and Fischer’s exact tests in SPSS version 26.0. Results: Females constituted 77.4% (n = 298) of all respondents, while 44.9% (n = 173) of the total reported a family history of gastrointestinal diseases. FFQ analysis showed varying consumption frequencies for different food groups. Functional abdominal pain and irritable bowel syndrome (IBS) were the highest reported FGIDs with a prevalence of 38.7% (n = 149) and 24.9% (n = 96), respectively. Statistical associations were found between different FGIDs and gender, age, household income, family members, and dietary variables such as fruit, vegetable, beverage and pulse consumption. Conclusion: FGIDs were found to be associated with a number of socio-demographic and dietary factors which calls for small scale and large scale attention to the issue. Results from the current study and further studies may help develop guidelines to manage these disorders in Pakistan. View Full-Text ►▼ Show Figures This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.