Hierarchy theory arose in the middle of the 1960s, as a result of a convergence from contributions of different disciplines that shared an interest for complexity, such as economy, chemistry, and biology. From the perspective of hierarchy theory, complexity is not considered either as a property of natural systems in themselves or as an exclusive property of the human mind, but rather as a property of questions posed by ourselves, as agents of knowledge, in the observational process. Complexity emerges, thus, in the relationship between natural systems and knowing subjects. This work carries out an analysis of the epistemological foundations of hierarchy theory, mainly addressing the possibility of grounding it in an anti-realist stance, such as van Fraassen’s constructive empiricism.