Systems mapping methods are increasingly used to study complex public health issues. Visualizing the causal relationships within a complex adaptive system allows for more than developing a holistic and multi-perspective overview of the situation. It is also a way of understanding the emergent, self-organizing dynamics of a system and how they can be influenced. This article describes a concrete approach for developing and analysing a systems map of a complex public health issue drawing on well-accepted methods from the field of social science while incorporating the principles of systems thinking and transdisciplinarity. Using our case study on HIV drug resistance in sub-Saharan Africa as an example, this article provides a practical guideline on how to map a public health problem as a complex adaptive system in order to uncover the drivers, feedback-loops and other dynamics behind the problem. Qualitative systems mapping can help researchers and policy makers to gain deeper insights in the root causes of the problem and identify complexity-informed intervention points.