Stenonychosaurus (type species S. inequalis) was named by C.M. Sternberg in 1932, based on a foot, fragments of a hand, and some caudal vertebrae from the Late Cretaceous of Alberta. A remarkable feature of these remains was the enlarged claw on the second toe, now recognized as characteristic of Deinonychosauria. Sternberg initially classified Stenonychosaurus as a member of the family Coeluridae within the theropod dinosaurs. Later, Sternberg (1951) speculated that since Stenonychosaurus had a "very peculiar pes" and Troodon "equally unusual teeth", they may be closely related. Unfortunately, no comparable specimens were available at that time to test the idea.

A more complete skeleton of Stenonychosaurus was described by D.A. Russell in 1969, which eventually formed the scientific foundation for a famous life-sized sculpture of Stenonychosaurus accompanied by its fictional, human-like descendant, the "dinosauroid". Stenonychosaurus became a well-known theropod in the 1980s, when the feet and braincase were described in more detail. It is sometimes listed as the "most intelligent" of dinosaurs. P.J. Currie, reviewing the known Troodontidae in 1987, reclassified Stenonychosaurus inequalis as a junior synonym of Troodon formosus. This synonomy has been widely adopted by other paleontologists, and therefore all of the specimens once called Stenonychosaurus are now referred to as Troodon in the recent scientific literature. Other taxa "lumped" into Troodon are Pectinodon bakkeri and Polyodontosaurus grandis, which, along with Stenonychosaurus inequalis may all be separate valid species, or belonging to one genus or species.