The Red Devils started the better of the two sides and dominated much of the first period.
In fact, Leah Galton had the ball in the back of the Blues' net inside the opening 20 seconds - but the goal was ruled out.
Man Utd continued to push for what would have been a deserved lead, but Chelsea ushered out a stalemate at the break.
Sam Kerr struck in the 68th minute to give her side the lead, following a much more composed display by the Blues after the restart.
Man Utd continued to push for their Wembley goal, but it wasn't meant to be as Chelsea claimed the win - and the Women's FA Cup.
Live commentary
Chelsea have won the Women's FA Cup!
Sam Kerr has given Chelsea the lead in the 68th minute!
The second half has begun.
Leah Galton of Manchester United had the ball in the back of the net within the first 30 seconds of play, but the goal was ruled out for offside.
The first half has begun.
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Match preview
Chelsea are up against Manchester United in this season's Women's FA Cup final at Wembley Stadium in London.
The match promises to be a blockbuster, featuring the top two sides in the Women's Super League.
To reach the final, Manchester United beat Brighton and Hove Albion 3-2, whereas Chelsea overcame Aston Villa 1-0.
Sam Kerr is the 'one to watch' in this clash, with five goals already to her name in the Women's FA Cup this term.
Manchester United duo Nikita Parris and Alessia Russo, with four and three goals in the competition thus far respectively, are another couple of stars.
The match is scheduled to get underway at 2.30pm BST.
