Program evaluation is an essential, but often neglected, activity in any transformational educational change. Competence by Design was a large-scale change initiative to implement a competency-based time-variable educational system in Canadian postgraduate medical education. A program evaluation strategy was an integral part of the build and implementation plan for CBD from the beginning, providing insights into implementation progress, challenges, unexpected outcomes, and impact. The Competence by Design program evaluation strategy was built upon a logic model and three pillars of evaluation: readiness to implement, fidelity and integrity of implementation, and outcomes of implementation. The program evaluation strategy harvested from both internally driven studies and those performed by partners and invested others. A dashboard for the program evaluation strategy was created to transparently display a real-time view of Competence by Design implementation and facilitate continuous adaptation and improvement. The findings of the program evaluation for Competence by Design drove changes to all aspects of the Competence by Design implementation, aided engagement of partners, supported change management, and deepened our understanding of the journey required for transformational educational change in a complex national postgraduate medical education system. The program evaluation strategy for Competence by Design provides a framework for program evaluation for any large-scale change in health professions education.