Urban transformations are complex, dynamic, and systemic societal phenomena that have many positive and negative consequences, including irreversible changes to land-use and loss of soil permeability, deforestation and accelerating losses of biodiversity, energy consumption and increasing volumes of green-house gas emissions, demographics and greater socio-economic inequalities, and accelerating incidences of non-communicable diseases. These omnipresent diseases (e.g., asthma, cancers, cardiovascular diseases, type 2 diabetes) have no cultural, geographical, or socio-economic boundaries and they impact all age groups including children and young adults. Local and national authorities North and South of the Equator, and international organizations and networks, have rarely responded effectively to children's health challenges in the context of rapid urban development. The purpose of this article is to describe and illustrate more effective approaches. It proposes new ideas, founded on collective thinking involving several disciplines and professions, and new working methods, founded on collaboration with community associations in civil society. Both promote shared understandings about the complex, dynamic, systemic, and emergent nature of urban health risks for children. The article explains why transdisciplinary contributions should be distinguished from multi-and inter-disciplinary contributions, and it presents examples of participatory action research in the WHO European region about children's health.