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Arsenal won the 2015 FA Cup.
The airline's deal will see England's showpiece domestic cup competition become known as The Emirates FA Cup from next season. The value has not been disclosed.
The FA has been looking for a new sponsor since Budweiser ended its three-year association with the competition last year.
Greg Dyke, chairman of The FA, said: "Emirates' commitment to our sport is evident and securing such an iconic and forward-thinking lead partner for The FA Cup is great news for us, the fans and for the whole game.
"The partnership will help take the tournament to new audiences, inspire interest in football from across the globe and allow us to continue our investment into the game at all levels."
Emirates Airline president Sir Tim Clark pointed to the FA Cup's "unrivaled heritage" and "global audience of more than 1.1 billion people" in his reasoning for the deal.
It was announced just a few hours before Arsenal beat Aston Villa 4-0 in the 2015 final at Wembley.