As its name suggests, the greater padloper is the largest of all the Homopus ("padloper") tortoises, but it is nonetheless tiny, averaging slightly over 10 cm in length – though males tend to be smaller. It has relatively large buttock tubercles. Like its close relative, H. areolatus (and unlike other padlopers), it has only four toes on its front feet as well as its hind feet.
Its shell ranges in colour from olive to reddish-brown, and is slightly flattened in both sexes. The shields tend to be separated by very thin white lines. In juveniles and adult males, the shields of the shell usually have slightly darker edges. Males can also be distinguished from females by being smaller, with longer tails. Males do not exhibit plastral concavity.
This species is sometimes confused with the Karoo padloper (H. boulengeri) which inhabits the Karoo region to the west. However greater padlopers can be distinguished not only by their larger size, but also by their nostrils which are below their eye level, by their having four toes on both their front and back feet, by the larger scales on their forelimbs, and by the darker rings around the shell scutes of many individuals.