BackgroundThe complexity of US healthcare has been increasing for many years, requiring clinicians and learners to understand care delivery systems in addition to clinical sciences. Thus, there has been a major push to educate faculty and trainees on healthcare functionality. This comes as hospitals expand into health systems requiring the help of more sophisticated expertise of departments such as operations excellence when problem-solving. As a medical student with a background in operations excellence, medical education leader and clinical administration leader all currently facilitating this transition, we wanted to reflect on the barriers we have experienced in clinical implementation of quality improvement projects and educating learners on the impact of operations excellence principles in their clinical education.MethodsThe ideas presented in this article were the result of a several collaborative discussion between the authors, on the key challenges to adopting operations excellence principles into health system science education. In an effort to add context to this reflection through the current body of research present, they supplemented a literature review on the topic which included 86 studies published between 2013 and 2021 regarding health systems science and healthcare leadership engagement in the USA. The themes that intersected between the literature review and the discussions were then expanded on in this paper.ResultsThrough this process, we identified four challenges: (1) the difference in thinking styles, which we term, ‘mental model differences’; (2) the strategic nature of process improvement projects and how that collides with physician priorities, or ‘the chess game of stakeholder engagement’; (3) the language and precise methodology, or ‘consistency of language and need for administrative resilience’ and (4) the issue of teaching these concepts or bridging the learning gap.’ConclusionIn an increasingly complex healthcare landscape, physicians and trainee’s need to bridge gaps between the mental models of administrative and clinical workflow.