Several research articles have reported the shortage of qualified anatomy teachers across different countries. This issue is being addressed by developing graduate anatomy training programs where students are taught the different anatomical sciences. These graduates will also need to be trained as educational scholars in order to face the challenges in their future careers as academics. To address this educational need, in this article we discuss the design and development of a new course in ‘Anatomy Pedagogy’ that we successfully integrated into a new innovative master’s program in human anatomy in our institution. This course was designed by utilizing the different principles of the scholarship of teaching and learning. In this article, the authors aim to outline the content of this course and analyse it in light of the scholarship of teaching and learning. This includes the learning outcomes, faculty-led learning, student-led teaching, teaching practicum and the different assessment techniques used on this course. Some of the principles used to analyse this course includes universal design for learning, teaching for understanding, assessment as learning and peer to peer learning. In the coming academic years, the authors aim to collect qualitative and quantitative data what will help inform the future delivery of this course.