Goniopholis was named by Owen (1842) [Owen describes this as a "subgenus" but does not indicate which genus it belongs to.]. It is the type genus of Goniopholinae. It was considered monophyletic by Karl et al. (2006).

It was assigned to Crocodilia by Owen (1842); to Saurii by Meyer (1845); to Crocodilidae by d'Orbigny (1849); to Amphicoelia by Owen (1860) and Owen (1861); to Goniopholinae by Nopcsa (1928); to Goniophididae by Carroll (1988); to Mesoeucrocodylia by Pol and Norell (2004); to Goniopholidae by Dollo (1884), Hay (1902), Delair (1958), Salisbury et al. (1999), Martin and Buffetaut (2012) and Pritchard et al. (2013); to Neosuchia by Ortega et al. (2000), Sereno et al. (2003), Turner (2006), Zaher et al. (2006), Larsson and Sues (2007), Fiorelli and Calvo (2008), Nascimento and Zaher (2011) and Sertich and O'Connor (2014); and to Goniopholididae by Cope (1875), Hay (1930), Buffetaut and Ingavat (1983), Tykoski et al. (2002), Schwarz (2002), Karl et al. (2006), Lauprasert et al. (2007), Andrade et al. (2011), Bronzati et al. (2012), Puértolas-Pascual et al. (2015), Martin et al. (2016) and Allain et al. (2022).