Higher education institutions (HEIs) are crucial in transitioning to sustainable, carbon-neutral societies. However, achieving sustainability in HEIs requires systemic transformation across governance, operations, teaching, and research. This paper presents a simulation model designed to enhance awareness and strategic decision-making regarding sustainability in HEIs. The model was developed within a European transnational project focusing on a Whole Institution Approach (WIA) to sustainability through systems thinking. By integrating feedback loops and dynamic interdependencies, the model allows HEIs to simulate and evaluate policies, assess long-term sustainability impacts, and identify leverage points for transformation. A hypothetical case study illustrates the model’s application, providing an interactive learning environment for stakeholders. The model highlights the importance of aligning policies, resource allocation, and cultural shifts within HEIs to address the green transition and stimulates reflection on mental models and the development of sustainability strategies.