Echinodon was named by Owen (1861). Its type is Echinodon becklesii. It was considered monophyletic by Butler et al. (2010), Sereno (2012).

It was synonymized subjectively with Sauraechinodon by Romer (1956); it was synonymized subjectively with Saurechinodon by Tatarinov (1964), Kuhn (1964), Romer (1966).

It was assigned to Dinosauri by Quenstedt (1882); to Lacertilia by Owen (1861), Owen (1861), Mansel-Pleydell (1888); to Dinosauria by Lydekker (1888); to Omosauridae by Huene (1909); to Scelidosauridae by Zittel (1890), Van Den Broeck (1900), Hennig (1915); to Scelidosaurinae by Nopcsa (1928); to Stegosauria by Delair (1960); to Stegosauridae by Nopcsa (1901), von Zittel (1911), Charig (1967); to Hypsilophodontidae by Thulborn (1970), Thulborn (1971); to Fabrosauridae by Galton (1972), Galton (1973), Thulborn (1974), Galton (1974), Galton (1974), Thulborn (1975), Galton (1978), Galton (1981), Weishampel and Weishampel (1983), Galton (1983), Milner and Norman (1984), Norman (1984), Russell (1984), Galton (1985), Buscalioni and Sanz (1987), Carroll (1988); to Thyreophora by Ensom et al. (1991); to Heterodontosauria by Olshevsky and Ford (1994); to Pachycephalosauria by Dieudonné et al. (2020); and to Heterodontosauridae by Sereno (1991), Sereno (1997), Ruiz-Omeñaca (2000), Norman and Barrett (2002), Norman et al. (2004), Chure et al. (2006), Pereda Suberbiola et al. (2006), Sánchez-Hernández et al. (2007), Naish and Martill (2007), Galton (2007), Naish and Martill (2008), Galton (2009), Butler et al. (2010), Sereno (2012), Hübner (2016), Madzia et al. (2018), Allain et al. (2022).