The airline has also unveiled a new-look winter schedule with two key business routes to London.
There will be three return flights daily to both Heathrow and Gatwick.
From March 2013, the carrier will also operate daily flights to Malaga, in Spain, and Faro, in Portugal.
Christoph Mueller, Aer Lingus CEO, said: “Northern Ireland’s vital London connections are secure. The two aircraft which we normally use in the winter for a mixture of sun destinations and Heathrow will be used for Heathrow and Gatwick with a third aircraft serving two European routes in the new-look summer schedule.”
Mueller said it was a “commercial decision” to move, adding: “George Best Belfast City Airport delivers a compelling location and a strong history of business flying.
“We believe the move will appeal to the 600,000 plus passengers annually who fly with us and especially the business traveller who now has a choice of two London airports with Aer Lingus.”
Aer Lingus said it expected transfer traffic to grow through both Heathrow and Gatwick.
The airline will start flying from George Best Belfast City Airport at the end of October.