Heterodontosaurus was named by Crompton and Charig (1962). Its type is Heterodontosaurus tucki. It is the type genus of Heterodontosauridae, Heterodontosaurinae. It was considered monophyletic by Butler et al. (2010) and Sereno (2012).

It was synonymized subjectively with Lycorhinus by Thulborn (1970), Thulborn (1972) and Thulborn (1974).

It was assigned to Ornithischia by Simmons (1965); to Hypsilophodontidae by Thulborn (1970); to Ornithopoda by Crompton and Charig (1962) and Swinton (1970); to Tianchungosauroidea by Zhao (1983); to Xiphosauridae by Sereno (1986); to Heterodontosauridae by Kuhn (1966), Romer (1966), Galton (1972), Charig and Crompton (1974), Galton (1974), Galton (1974), Bonaparte (1976), Santa Luca et al. (1976), Anderson and Cruickshank (1978), Santa Luca (1980), Colbert (1981), Weishampel and Weishampel (1983), Olsen and Galton (1984), Norman (1984), Maryanska and Osmólska (1985), Battail (1986), Carroll (1988), Norman (1989), Benton (1990), Weishampel and Witmer (1990), Olshevsky and Ford (1994), Chure et al. (1994), Smith (1997), Sereno (1998), Báez and Marsicano (2001), Norman et al. (2004), Knoll (2005), Gand et al. (2007), Butler et al. (2007), Butler et al. (2008), Butler et al. (2008), Butler and Zhao (2009), Butler et al. (2010), Langer et al. (2010), Norman et al. (2011), Porro et al. (2011), Han et al. (2012), Hübner (2016) and Madzia et al. (2018); and to Heterodontosaurinae by Sereno (2012) and Dieudonné et al. (2020).