Martial picked up the injury against Fulham in Manchester United's final Premier League game of the season last Sunday. The Red Devils won 2-1 to finish third on the table.
United manager Erik Ten Hag says his side play better when Martial is on the pitch but the Frenchman has had a stop-start season due to niggling injuries.
Martial has made 29 appearances across all competitions this term, scoring nine goals and providing three assists.
United said in a statement: “Anthony Martial is out of Saturday’s Emirates FA Cup final against Manchester City due to injury.
“The France international strained his hamstring towards the end of Sunday’s 2-1 win against Fulham at Old Trafford.
“Assessments have since revealed a muscle tear that rules the 27-year-old out of the Wembley showdown.”
Having already won the Carabao Cup earlier in the season, United will be looking to complete the domestic cup double by beating their city rivals at Wembley.
Victory for Manchester United will also deny City the chance the win a famous treble this season, with Pep Guardiola's side facing Inter Milan in the Champions League final next week, having already won the Premier League for the third consecutive campaign.
