John MacNaughton or variant spellings, may refer to:

• John A. MacNaughton (1945–2013), a Canadian investment banker
• John H. MacNaughton (born 1929), an American bishop
• John McNaughton (born 1950), an American film and TV director
• John McNaughton (government official) (1921–1967), American official
• Jock McNaughton (1912–1986), a Scottish professional footballer
• John Macnaghten (1722–1761), known as Half-Hanged MacNaghten, an Anglo-Irish convicted murderer
• Jon McNaughton, an American painter of conservative political themes