The notion of “hierarchy” is one of the most commonly posited organizational principles in systems neuroscience. To this date, however, it has received little philosophical analysis. This is unfortunate, because the general concept of hierarchy ranges over two approaches with distinct empirical commitments, and whose conceptual relations remain unclear. We call the first approach the “representational hierarchy” view, which posits that an anatomical hierarchy of feed-forward, feed-back, and lateral connections underlies a signal processing hierarchy of input-output relations. Because the representational hierarchy view holds that unimodal sensory representations are subsequently elaborated into more categorical and rule-based ones, it is committed to an increasing degree of abstraction along the hierarchy. The second view, which we call “topological hierarchy", is not committed to different representational functions or degrees of abstraction at different levels. Topological approaches instead posit that the hierarchical level of a part of the brain depends on how central it is to the pattern of connections in the system. Based on the current evidence, we argue that three conceptual relations between the two approaches are possible: topological hierarchies could substantiate the traditional representational hierarchy, conflict with it, or contribute to a plurality of approaches needed to understand the organization of the brain. By articulating each of these possibilities, our analysis attempts to open a conceptual space in which further neuroscientific and philosophical reasoning about neural hierarchy can proceed.