Protypotherium was slightly larger than a rabbit, measuring about 40 centimetres (1.3 ft) in length. The body and legs as well as the tail of this animal were relatively long, while its neck was short. It probably resembled a rodent, possessing slender limbs with clawed feet. Its rat-like skull contained a set of 44 unspecialized teeth.
From the shape of its claws, Protypotherium would have been adept at digging and likely took over the burrows of other animals. It is hypothesized[by whom?] that, while Protypotherium was chiefly herbivorous, it probably also ate carrion.