Unlike later, more derived ornithomimosaurs, Harpymimus still possessed teeth, although they appear to have been restricted to the dentary of the lower jaw.

[3] In a 2005 article, Kobayashi and Barsbold diagnosed Harpymimus based on a number of anatomical characteristics, including eleven teeth in the front of the lower jaw (dentary), the transition between anterior and posterior tail vertebrae taking place at the eighteenth caudal, a triangular-shaped depression above the dorsal surface of a ridge on the shoulder blade (scapula) above the shoulder joint, a low ridge above a distinctive depression along back edge of the shoulder blade, and a small but deep collateral ligament fossa on the lateral condyle of metacarpal III (a hand bone).

The teeth of Harpymimus differ from those of another basal ornithomimosaur, Pelecanimimus polyodon, in that they are restricted to the dentary, are cylindrical and separated by interdental plates, and number at least ten and perhaps eleven per side.

The small teeth of Harpymimus were probably used only for grabbing and holding food items, unlike those of many other theropods, which were adapted to cutting or piercing prey.

Other basal traits are the very short first metacarpal in the hand and a third metatarsal that, though pinched at the top, is at that point not excluded form the front surface of the metatarsus, so that the foot is not arctometatarsalian.