Procolophonia was named by Seeley (1888) [Whether the taxon is extinct or not depends on exlusion or inclusion of turtles, respectively.]. It is not extant. Its type is Procolophonoidea. It was considered monophyletic by Laurin and Reisz (1995) and Lee (1997).

It was reranked as the order Procolophonia by Osborn (1903), Osborn (1904), Roxo (1937), Huene (1954), Olson (1962) and Olson (1966); it was reranked as the order Procolophonii by Jaekel (1910); it was corrected as Procolophonii by Jaekel (1911); it was reranked as the infraorder Procolophonia by Haughton and Brink (1954); it was reranked as the unranked clade Procolophonia by Gauthier et al. (1988), Gauthier et al. (1989), Laurin and Reisz (1995), deBraga and Reisz (1996), Lee (1997), Reisz and Scott (2002) and Modesto and Damiani (2003).

It was assigned to Diaptosauria by Osborn (1903) and Osborn (1904); to Protorosauria by Jaekel (1910); to Gephyrostegi by Jaekel (1911); to Cotylosauria by Broom (1913); to Cotylosauria by Roxo (1937); to Diadecta by Olson (1947); to Reptiliomorphoidea by Huene (1954); to Diadectimorpha by Haughton and Brink (1954); to Diadectomorpha by Kuhn (1966); to Anapsida by Olson (1966); to Cotylosauria by Daly (1973), Colbert and Kitching (1975) and Lavina (1983); to Captorhinida by Carroll (1988); to Amniota by Gauthier et al. (1989); to Parareptilia by Olson (1962), Gauthier et al. (1988) and Laurin and Reisz (1995); to Ankyramorpha by deBraga and Reisz (1996); to Helpme by Small (1997); to Procolophonomorpha by Lee (1997); to Parareptilia by Reisz and Scott (2002) and Modesto and Damiani (2003); and to Procolophonida by Ivakhnenko (2008).