Background: Digestive health plays a crucial role in pediatric growth and development. Indonesia, as a developing nation, grapples with widespread infectious gastrointestinal (GI) ailments, particularly in rural areas. Concurrently, urban regions are experiencing an increase in non-infectious GI conditions due to recent socio-economic shifts. Current data on GI health among Indonesian children remains scarce and fragmented. Objective: The objective of this scoping review was to elucidate the present state of GI health among Indonesian children under five years of age. Methods: A scoping review was carried out to assess the current landscape of GI health in Indonesia. The review encompassed studies published between 2012 and 2022, with database searches performed on PubMed and Google Scholar from April 1st to 14th, 2022, using relevant keywords. Results: The review identified 58 studies meeting the inclusion criteria. Analysis of these studies revealed five key themes in pediatric GI health: [1] epidemiology, [2] infectious and non-infectious GI disease, [3] diagnostic, [4] interventions, and [5] short-term and long-term effects. Conclusion: The review identified diarrhea, gastroenteritis, colitis, soil-transmitted helminth infections, regurgitation, constipation, and colic as the most prevalent GI issues among Indonesian children under 5. The study highlights the interconnected nature of gastrointestinal diseases, malnutrition, and gut microbiota. It underscores the importance of proper dietary habits and adequate early nutrition, including both macro and micronutrients, with particular emphasis on fiber intake, in fostering a healthy gut microbiome essential for optimal GI function. © 2024 The Author(s). Published by Bentham Open.