Aer Lingus Chief Executive Dermot Mannion resigned this morning with immediate effect.
Mr Mannion joined the airline in 2005.
The airline's chairman, Colm Barrington, will take over Mr Mannion's position until a successor is appointed.
When contacted by RTÉ, Mr Barrington said: 'Dermot Mannion and myself have had a very good relationship and I am sad to see him go.'
He said he would not be making any further comment on the matter.
Aer Lingus, which made a loss of almost €120m in 2008, says the search for a new chief executive has begun.
Mr Mannion's departure will come as a surprise given that life at the airline today is relatively calm compared to recent times.
He signed a three-year contract in August 2005 and has been on a rolling one-year contract since autumn of last year.
He has steered the airline out of State ownership, fended off two hostile take-over bids from Ryanair and controversially axed the Shannon to Heathrow service.
There has been a constant focus on cost against a background of unpredictable fuel prices, strike threats, cut-throat competition and economic downturn in its key markets of Europe and the US.
Hundreds of employees have left the airline.
The airline is expected to make a loss this year too. Sources at the airline say Mr Mannion's decision to leave was amicable.
Among the internal favourites to succeed Mr Mannion are deputy chief Niall Walsh and finance boss, Sean Coyle, who recently joined the airline from Ryanair.
