The move has been welcomed by political and business leaders in the midwest.
The new service will begin on 4 February and will operate twice daily with return flights from both points for five days and one service at the weekend.
It will offer Shannon customers access to a major hub operated by CityJet's parent company Air France-KLM with flights to 248 international destinations.
Aer Lingus is set to end its Shannon to Heathrow service in January.
Welcoming the new service, Minister for Transport Noel Dempsey said CityJet's presence in Shannon would help to grow business and attract new industries and visitors.
On behalf of the business community in the mid west, the Atlantic Connectivity Alliance said it was a major boost to their efforts to keep international connectivity in the west and midwest.
