Juniac helped Europe's second biggest airline group return to profit last year for the first time since 2008, but his four-year spell at the helm was also marked by acrimonious relations with pilots.
On announcing the surprise move, the Franco-Dutch company said it was hoping to appoint De Juniac's replacement from August 1 at the latest.
Around 0720 GMT, the company's shares were down nearly seven per cent on an overall firmer Paris stock exchange.
De Juniac took charge at Air France in 2011, becoming chairman of Air France-KLM a year later.
He leaves the company on the track to recovery but still in a fragile position, facing tough competition from Gulf-based competitors for long-haul business and from low-cost rivals for short-haul market share.
The return to profits, announced in February, came after a major restructuring to boost productivity and a 2014 strike by Air France pilots that was one of the longest in the company's history.
Management in January unveiled a new 2017-2020 growth plan that will include 1,600 voluntary departures by the end of next year, according to union sources.
