While systems thinking has been generally acknowledged as important to the field of health policy and systems research (HPSR), it remains underutilized. In particular, systems thinking has been perceived as predominantly conceptual, with fewer applications of systems thinking documented. This commentary makes three key points, namely that (1) advances in applied systems thinking in HPSR have been hindered by an imprecision in terminology, conflating ‘[health] systems approaches’ with complex adaptive systems theory; (2) limited examples of applied systems thinking have been highlighted and recognized in research, but have not been fully and equally appreciated in policymaking and practice and (3) explicit use of theory, long-term research-policy collaborations and better documentation of evidence can increase the use and usefulness of applied systems thinking in HPSR. By addressing these matters, the potentials of systems thinking in HPSR can be truly unlocked.