A number of partial fossil remains of Secodontosaurus have been identified from its characteristic long skull and jaws. The postcranial skeletal material from different individuals includes parts of the backbone with clear evidence of a tall sail very similar to that of Dimetrodon. The limbs and tail are incompletely known but probably resembled those of Dimetrodon as well. Like Dimetrodon, Secodontosaurus would have had a short neck, robust body, short limbs, and a long tail. In light of such similarities, some skeletal remains with missing or fragmentary skulls that were previously identified as Dimetrodon may in fact belong to Secodontosaurus. A key noncranial difference can be found in the axis neck vertebra, which has a tall and broad neural spine in Dimetrodon but has a lower neural spine in Secodontosaurus.
Robert R. Reisz and others described the skull in detail in 1992, based mostly on a nearly complete skull specimen about 27 cm long, preserved with a left mandible. In addition to the long, low skull and nearly uniform size of the teeth that contrast with Dimetrodon, the anterior teeth of the upper jaw are slanted back and those of the lower jaw are directed forward for grasping prey. Its rather crocodile-like skull suggests that Secodontosaurus could have been semi-aquatic and may have fed on fish and small swimming amphibians. However, Reisz and his coauthors noted that a tall sail would seem to be a hindrance in pursuit of quick-moving creatures underwater. Instead, the long, narrow snout with forward slanting teeth at the mandible tip might have allowed Secodontosaurus to probe after small animals hiding in burrows and other tight spaces.