Troodon was named by Leidy (1856). It is the type genus of Troodontinae. It was considered monophyletic by Currie (2000).

It was synonymized subjectively with Saurornithoides by Carpenter (1982); it was considered a nomen vanum by Sues (1977).

It was assigned to Sauria by Leidy (1860); to Goniopoda by Cope (1870); to Goniopoda by Cope (1877); to Lacertilia by Leidy (1856) and Lambe (1902); to Megalosauridae by Zittel (1890), Nopcsa (1901) and Hay (1902); to Lacertilia by Lambe (1905); to Ankylosauridae by Brown (1908) and Huene (1909); to Nodosauridae by Hennig (1915); to Scelidosaurinae by Huene (1927); to Acanthopholidae by Nopcsa (1928) and Nopcsa (1928); to Acanthopholinae by Nopcsa (1929) and Nopcsa (1931); to Theropoda by Russell (1946); to Coeluridae by Romer (1956), Parsch (1963), Romer (1966) and Steel (1970); to Deinodontidae by Wolberg (1980); to Saurornithoididae by Carroll (1988); to Troodontidae by Lull (1924), Gilmore (1924), Hay (1930), Russell (1930), Gilmore (1931), Sternberg (1933), Brown and Schlaikjer (1943), Sternberg (1945), Russell (1948), Sternberg (1951), Bohlin (1953), Kuhn (1966), Langston (1975), Langston (1976), Gauthier (1986), Currie (1987), Currie (1987), Paul (1988), Barsbold (1988), Currie et al. (1990), Currie (1992), Russell and Dong (1994), Currie and Zhao (1994), Currie and Peng (1994), Chure (1994), Nessov (1995), Varricchio (1997), Eberth (1997), Sereno (1997), Sereno (1998), Currie (2000), Norell et al. (2000), Eberth et al. (2001), Currie and Dong (2001), Peng et al. (2001), Sankey et al. (2002), Rauhut (2003), Makovicky et al. (2003), Senter et al. (2004), Makovicky and Norell (2004), Smith (2007), Longrich (2008), Bever and Norell (2009), Norell et al. (2009), Fiorillo et al. (2009), Godefroit et al. (2009), Lü et al. (2010), Zanno et al. (2011), Porfiri et al. (2011), Brown and Druckenmiller (2011), Xu et al. (2012), Larson and Currie (2013), Godefroit et al. (2013), Hendrickx and Mateus (2014), Tsuihiji et al. (2014), Williamson and Brusatte (2014) and Gianechini et al. (2017); and to Troodontinae by van der Reest and Currie (2017) and Sellés et al. (2021).