Wannanosaurus is one of the most primitive pachycephalosaurs yet discovered, as it possessed neither the pitted cranium nor the nearly enclosed skull that were the hallmarks of its more derived brethren. Its skull was flattened on top, markedly different than the domed heads on more familiar pachycephalosaurs such as Pachycephalosaurus. But how different this feature was is a matter of some debate.

One side holds that this flat, table-top skull is a derived character within the Pachycephalosauria. This means that, early on in pachy evolution, one group evolved flat heads while another group begat dome-headed descendants. The flat-heads are termed homalocephalids (after Homalocephale, the first flat-head named); the dome-heads are called pachycephalosaurids (after Pachycephalosaurus). To clear up all the "pachycephalos" being thrown about: the flat-heads and dome-heads are all pachycephalosaurians (or pachycephalosaurs, to save a few letters) but only the dome-heads are pachycephalosaurids. If flat-headedness is a trait derived from normal-headedness with no connection to dome-headedness, then Wannanosaurus is a homalocephalid in good standing.

But, what if dome-heads evolved from flat-headed ancestors? In this case flat-headedness is a primitive character compared to dome-headedness, and it would no longer be valid to consider flat-heads as a discrete group apart from dome-heads. For example, Wannanosaurus had a flat head, like Homalocephale. But it had large supratemporal fenestrae (holes in the skull roof through which jaw muscles pass), like the dinosaurs most closely related to pachycephalosaurs. And Wannanosaurus had a granulated skull, unique unto itself, which might be a transitional character between the unornamented skulls of pachycephalosaur relatives and the pitted skulls of other pachycephalosaurs.

Homalocephale had a flat head, like Wannanosaurus. But it had small supratemporal fenestrae and a pitted skull, like pachycephalosaurids. Using these characters, it seems that Homalocephale was more closely related to, or shared a more recent common ancestor with, pachycephalosaurids than it did with Wannanosaurus. In this scenario, Wannanosaurus and Homalocephale do not form a true evolutionary group separate from the pachycephalosaurids, but represent two grades of development approaching the dome-headed condition.