The development of a program assessment system is an opportunity for faculty to 1) think deeply about how courses work together over a full academic program to facilitate course, program, and institutional learning objectives and 2) to create meaningful assessment strategies that help improve student learning. Yet assessment in academia is often viewed as an outward-facing, accreditation driven add-on to faculty workload, perhaps because little guidance is available on how to develop meaningful, learner-centered assessment systems. In this paper, we describe a systems thinking approach where faculty view their institution, programs, and courses as integrated systems and use the insights this provides to design a program level assessment system. Applying systems thinking principles in assessment provides a framework for bridging the course-level, in-class assignments to larger program and institutional assessment, increasing efficiency and minimizing faculty effort. The data the resulting well-designed, learner-centered program assessment system provides drives curricular change to facilitate increased achievement of student learning outcomes, making assessment meaningful for its stakeholders.