Owen originally classified Echinodon as a herbivorous lizard, he revised its placement to one within Dinosauria.
Echinodon was considered an intermediate, potentially ornithischian, dinosaur until it was referred by Franz Nopcsato the clade Scelidosaurinae within Stegosauridae in 1928 based on a tall coronoid process and tapering teeth, both of which are considered widespread within ornithischians.
Isolated dermal armour found in the Purbeck Beds was referred to Echinodon on the basis of a stegosaurian classification by Justin Delair in 1959, although these have since been reassigned to solemydid turtles.

Classifications of many basal ornithischians were reviewed by Richard Thulborn in 1971, where he placed Echinodon within Hypsilophodontidae: derived from Triassic forms lacking canines (termed "fabrosaurs"), close to the Jurassic genera Laosaurus and Nanosaurus, and more primitive than the Cretaceous genera Hypsilophodon, Parksosaurus and Thescelosaurus.
Galton published a rebuttal the following year, disagreeing with Thulborn's use of Hypsilophodontidae.
As teeth in the premaxilla, one of Thulborn's diagnostic traits for the family, were a primitive feature, Galton argued they should not be used to classify ornithopods.
Instead, Fabrosaurus and Echinodon were united in the new family Fabrosauridae based on laterally positioned teeth, and removed from Hypsilophodontidae.
Galton followed up on this classification with the naming of the genus Lesothosaurus in 1978, and along with its description reviewed the anatomy of multiple basal ornithischian genera, including Echinodon, Nanosaurus and Fabrosaurus.
All but Echinodon were definitively referred by him to Fabrosauridae, although the placement of Echinodon was questionable as it also bore similarities to the clade Heterodontosauridae, known to possess enlarged canine teeth as well.
However, Galton considered a fabrosaurid identity more likely as the teeth of the taxon lack flat wear facets.

Sereno was the first to reclassify Echinodon as a member of the family Heterodontosauridae.
In 1991, he revised the cranial anatomy of Lesothosaurus, and compared it to a large number of other basal ornithischians.
The teeth of Echinodon, in fact,  were interpreted to possess flat wear facets on its teeth, as well as having teeth inset from the edge of the maxilla like in ornithischians more derived than Lesothosaurus.
As these were what was suggested to unite the genus with "fabrosaurs", Sereno considered Echinodon to be a heterodontosaurid based on the presence of canines and arched gaps in the front of the tooth row.
Heterodontosaurus, Abrictosaurus and an undescribed form from the Kayenta Formation were also placed within the family.
Norman and Barrett redescribed Echinodon in 2002 and supported the heterodontosaurid classification but instead referred it to the clade based on the lacking foramina on tooth-bearing bones and possessing denticles restricted to the top third of the crown.

Although a placement as a heterodontosaurid for Echinodon has been supported in further analyses including some of the first phylogenetic analyses of ornithischians, the placement of the family itself has changed over time.
The family, either excluding Echinodon as in Thulborn's 1971 study, or including the genus as in Galton's and Sereno's work, was originally considered to be a group of basal ornithopods more derived than ankylosaurs and stegosaurs.
Further research, including the extensive phylogenetic analysis of British palaeontologist Richard J. Butler and colleagues in 2008 supported heterodontosaurids as the most basal ornithischians instead.
A revised analysis by Butler et al.
in 2011 also resolved a basal placement for heterodontosaurids, and resolved internal relationships of the family, with Echinodon being a basal genus in the family along with Abrictosaurus as well.
Following additional analysis by South American palaeontologist Diego Pol and colleagues in 2011, Echinodon was resolved as a basal ornithischian, yet not within the family Heterodontosauridae.
Pol et al.
considered that th
Owen originally classified Echinodon as a herbivorous lizard, he revised its placement to one within Dinosauria. Echinodon was considered an intermediate, potentially ornithischian, dinosaur until it was referred by Franz Nopcsato the clade Scelidosaurinae within Stegosauridae in 1928 based on a tall coronoid process and tapering teeth, both of which are considered widespread within ornithischians. Isolated dermal armour found in the Purbeck Beds was referred to Echinodon on the basis of a stegosaurian classification by Justin Delair in 1959, although these have since been reassigned to solemydid turtles.
Classifications of many basal ornithischians were reviewed by Richard Thulborn in 1971, where he placed Echinodon within Hypsilophodontidae: derived from Triassic forms lacking canines (termed "fabrosaurs"), close to the Jurassic genera Laosaurus and Nanosaurus, and more primitive than the Cretaceous genera Hypsilophodon, Parksosaurus and Thescelosaurus. Galton published a rebuttal the following year, disagreeing with Thulborn's use of Hypsilophodontidae. As teeth in the premaxilla, one of Thulborn's diagnostic traits for the family, were a primitive feature, Galton argued they should not be used to classify ornithopods. Instead, Fabrosaurus and Echinodon were united in the new family Fabrosauridae based on laterally positioned teeth, and removed from Hypsilophodontidae. Galton followed up on this classification with the naming of the genus Lesothosaurus in 1978, and along with its description reviewed the anatomy of multiple basal ornithischian genera, including Echinodon, Nanosaurus and Fabrosaurus. All but Echinodon were definitively referred by him to Fabrosauridae, although the placement of Echinodon was questionable as it also bore similarities to the clade Heterodontosauridae, known to possess enlarged canine teeth as well. However, Galton considered a fabrosaurid identity more likely as the teeth of the taxon lack flat wear facets.
Sereno was the first to reclassify Echinodon as a member of the family Heterodontosauridae. In 1991, he revised the cranial anatomy of Lesothosaurus, and compared it to a large number of other basal ornithischians. The teeth of Echinodon, in fact,  were interpreted to possess flat wear facets on its teeth, as well as having teeth inset from the edge of the maxilla like in ornithischians more derived than Lesothosaurus. As these were what was suggested to unite the genus with "fabrosaurs", Sereno considered Echinodon to be a heterodontosaurid based on the presence of canines and arched gaps in the front of the tooth row. Heterodontosaurus, Abrictosaurus and an undescribed form from the Kayenta Formation were also placed within the family. Norman and Barrett redescribed Echinodon in 2002 and supported the heterodontosaurid classification but instead referred it to the clade based on the lacking foramina on tooth-bearing bones and possessing denticles restricted to the top third of the crown.
Although a placement as a heterodontosaurid for Echinodon has been supported in further analyses including some of the first phylogenetic analyses of ornithischians, the placement of the family itself has changed over time. The family, either excluding Echinodon as in Thulborn's 1971 study, or including the genus as in Galton's and Sereno's work, was originally considered to be a group of basal ornithopods more derived than ankylosaurs and stegosaurs. Further research, including the extensive phylogenetic analysis of British palaeontologist Richard J. Butler and colleagues in 2008 supported heterodontosaurids as the most basal ornithischians instead. A revised analysis by Butler et al. in 2011 also resolved a basal placement for heterodontosaurids, and resolved internal relationships of the family, with Echinodon being a basal genus in the family along with Abrictosaurus as well. Following additional analysis by South American palaeontologist Diego Pol and colleagues in 2011, Echinodon was resolved as a basal ornithischian, yet not within the family Heterodontosauridae. Pol et al. considered that th
Echinodon