The 31-year-old forward, who returned to Everton from Manchester United in July, struck in the 35th minute at the Etihad Stadium, steering Dominic Calvert-Lewin's low cross between the legs of City goalkeeper Ederson.
He is only the second player to have reached the 200-goal milestone in the post-1992 Premier League era after Alan Shearer, who scored 260 goals for Blackburn Rovers and Newcastle United.
Having scored the only goal of Everton's opening fixture against Stoke City, it was Rooney's second goal of the season.
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