It was named by American paleontologist Everett C. Olson in 1951 on the basis of a holotype fossil that included a weathered skull, lower jaws, vertebrae, and part of the pectoral girdle.

[1] The fossil was discovered in a conglomerated deposit of the Early Permian Vale Formation near the town of Vera in Knox County, Texas.

The specimen was found in a nodule of rock that had broken, and much of the surface of the skull had weathered away.

Olson only tentatively assigned Waggoneria to Seymouriamorpha, noting other similarities with diadectomorphs and procolophonians.

Several other fossils found from the Vale Formation share similar features with Waggoneria but differ slightly in size and morphological detail.