Just a decade ago Vision and Change in Undergraduate Biology Education: A Call to Action was released, catalyzing several initiatives to transform undergraduate life sciences education. Among these was the Partnership for Undergraduate Life Sciences Education (PULSE), a national organization commissioned to increase the adoption of Vision and Change recommendations within academic life sciences departments. PULSE activities have been designed based on the recognition that life sciences departments and faculty are embedded within institutions of higher education which, similar to other large organizations, are complex systems composed of multiple, interconnected subsystems. The organizational change research suggests that effecting large-scale changes (e.g., undergraduate STEM education transformation) may be facilitated by applying systems thinking to change efforts. In this paper we introduce the approach of systems thinking as a professional development tool to empower individual STEM faculty to effect department-level transformation. We briefly describe a professional development experience designed to increase life sciences faculty members' understanding of systems thinking, present evidence that faculty applied a systems thinking approach to initiate department-level change, and discuss the degree to which transformation efforts were perceived to be successful. Though focused on faculty in the life sciences, our findings are broadly transferable to other efforts seeking to effect change in undergraduate STEM education.