[1] Robert M. Sullivan however, in 2006 disputed the pachycephalosaur classification, finding "few of the features [...] are characteristic of pachycephalosaur teeth," citing the lack of serrations on the teeth, and concluding the specimens are "too incomplete for identification".

He considers the taxon a nomen dubium, and a non-pachycephalosaurid ornithischian.

[2] In 2024, a comprehensive analysis of early ornithischian evolution found Ferganocephale to be most similar to Chaoyangsauridae in overall morphology but refrained from referring it to this clade based on its lack of denticles and strength of the cingulum.

[3] The type species, Ferganocephale adenticulatum, was first described by Averianov, Martin, and Bakirov in 2005, and is based solely on teeth from the Balabansai Svita in Fergana Valley, Kyrgyzstan, dating to the Callovian.

The genus name combines the name of location it was found with the Greek kephale, "head", a reference to the presumed pachycephalosaurian affinities.