Cities present many opportunities to improve socio-ecological sustainability through efficiencies of scale and access to resources and services. These benefits are often compromised by rapidly increasing urban populations demanding energy, water, resources and food that are sourced, produced and transported from rural areas in unsustainable ways. A systems level approach to understanding the complex challenges cities face is required to strategically plan for the future. Rooftop agriculture is one measure that can help address many sustainability problems cities are currently faced with. Our research aims to identify the role rooftop agriculture can play in moving society towards sustainability, the challenges it currently faces that may prevent it from being widely implemented, and how to overcome these challenges. To structure our research, we used the Framework for Strategic Sustainable Development (FSSD), a scientifically rigorous and peer reviewed model designed to manage the complexity of planning and decision-making towards sustainability. The culmination of this paper was the creation of a Sustainable Rooftop Agriculture Guide, a practical resource that can help city stakeholders determine how to best use rooftop agriculture in their movement towards sustainability.