More than 40,000 people packed into Wembley to watch the final on what was the 100th anniversary of women's being banned from playing the game.
The quality of Emma Hayes' side was superb as Arsenal proved no match with the deadly Fran Kirby and Sam Kerr double firing the Blues to the treble.
The 2020/21 FA Cup had been delayed due to the coronavirus pandemic.
Kirby put Chelsea a goal ahead just three minutes into the game as Hayes' side raced out of the blocks.
Arsenal failed to clear the ball and Kirby was able to race through on goal and made no mistake one-on-one with the goalkeeper.
Chelsea dominated the opening exchanges and both Kirby and Sam Kerr had chances to double their lead, but were thwarted by goalkeeper Manuela Zinsberger.
Both teams had penalty shouts turned down in the first half, but saw their appeals waved away.
Arsenal grew into the game more as the half progressed, but the Blues were good for their lead at the break.
Kerr grabbed a deserved second in the 57th minute as her shot caught Zinsberger flat footed and the ball went in at her near post.
Kerr then made sure of the result by scoring an outrageous chip over the Arsenal goalkeeper to make it 3-0.