Air pollution is an unseen threat to children’s health because it may increase the risk of respiratory infection, atopy, and asthma, and also alter gut microbiota compositions. The impact of air pollution on children’s health has not been firmly established. A literature review followed by a series of discussions among experts were performed to develop a theoretical framework on how air pollution could affect various bodily organs and functions in children. We invited experts from different backgrounds, such as paediatricians, nutritionists, environmental health experts, and occupational health experts, to provide their views on this matter. This report summarizes the discussion of multidisciplinary experts on the impact of air pollution on children’s health. The report begins with a review of air pollution’s impact on allergy and immunology, neurodevelopment, and cardiometabolic risks, and ends with the conceptualization of a theoretical framework. While the allergic and immunological pathway is one of the most significant pathways for air pollution affecting children’s health in which microbiotas also play a role, several pathways have been proposed regarding the ability to affect neurodevelopment and cardiometabolic risk. Further research is required to confirm the link between air pollution and the gut microbiota pathway. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.