It is expected that by 2030, more than 60% of the world’s population will be living within an urban area. To inform future urban health system governance in expanding urban areas, we propose the Urban Health System Governance Framework that identifies health policy co-benefits between SDG 3 (Good Health and Well-being) and SDG 11 (Sustainable Cities and Communities). We utilize two case studies to supplement our framework. Our first case study describes the Youth at a Healthy Weight (Jongeren op Gezond Gewicht – JOGG) intervention in the Netherlands. Our second case study describes the Barcelona Superblocks, which consist of amalgamations of blocks throughout the city to improve the habitability of public spaces, sustainable mobility, urban green, and promote residents’ participation and co-responsibility. Two important themes necessary to understand co-benefits between the two SDGs emerged. First, achieving SDG 11, that is making cities healthy, sustainability, inclusivity, resilience, are prerequisites to achieving good health and wellbeing. Second, addressing health inequities should be a strong priority to ensure urban growth is sustainable, inclusive, and resilient, and to promote equity, the health system and other urban governance structures must work together to create strong intersectoral collaboration.