Janaillac reportedly stepped down over a pay dispute with staff and the French government’s rejection of a bailout for the airline, the Financial Times reports.
On Friday Janaillac said he would resign after losing a vote over pay that was intended to end a series of strikes.
A replacement will be chosen during a board meeting on May 15.
Yesterday (Monday) shares in the carrier fell by as much as 14%, recovering to 10% by the end of the day.
Full-year results will also be hit, the group said.
Unions had wanted a larger upfront percentage and no conditions on further raises after being offered a 7% pay increase over four years. The strikes are continuing this week.
The French government, which owns 14.3% of the company, said Air France needed to reform or its survival would be at stake.
Delta and China Eastern are the next largest shareholders.