The stock slumped as much as 8.6% as the announcement of Mr de Juniac’s departure, a year after he secured a new contract, leaves Air France-KLM rudderless.
The shares later rallied to pare losses to a 3% drop on the day. They are still up 13% this year and values the airline at €2.38bn.
Mr de Juniac, who will leave by August to run the International Air Transport Association, said his successor must press on with restructuring plans while finding a way to win pilot backing.
Analysts say his exit at just 53 comes as a blow after he helped Air France-KLM snap four years of losses in 2015.
“We expect no more progress with unions in 2016,” Kepler Chevreux analyst Ruxandra Haradau-Doser said, adding that Mr de Juniac’s departure is “clearly negative news”.
Mr de Juniac had sought to build his strategy around shifting short-haul Air France flights that don’t connect with lucrative long-haul trips.
Labour grief culminated in violence last October, when senior managers fled a works council meeting over a fence with their clothing in shreds.