Concerns are growing over the ability of the modern food system to simultaneously achieve food security and environmental sustainability in the face of global change. Yet, the dominant tendency within university settings to conceptualize and address diverse food system challenges as separate, disconnected issues is a key barrier to food system transformation. To address this fragmented approach, educators in North American institutes of higher education have begun new degree programs, specializations and certificates related to food systems. These programs, which we term sustainable food system education (SFSE) programs, have a common goal: to support post-secondary students across a range of disciplines in developing the knowledge, skills and dispositions to effectively address complex challenges in the food system. Graduates of these programs will be able to engage in collective action towards transforming the food system. As educators participating in flagship SFSE programs, we identify common pedagogical themes evident in SFSE programs, including our own. We then propose a signature pedagogy (SP) for sustainable food systems education. Signature pedagogies are conceptual models that identify the primary elements by which professional education in a specific field is designed, structured and implemented. On the basis of our analysis of SFSE programs, we identified systems thinking, multi-, inter- and trans-disciplinarity, use of experiential learning approaches and participation in collective action projects as central themes within a SFSE SP. By making these themes and their function explicit within a pedagogical framework, we seek to spur critical and creative thought regarding challenges of professional education in the field of sustainable food systems. Scholars and practitioners are encouraged to review, critique and implement our framework to advance the dialogue on SFSE theory and practice.