He succeeds Patrick de Castelbajac, who will become company secretary and chief of staff, as well as a member of the executive committee of ATR shareholder Airbus.
The appointment will take effect from November 1, 2016.
In the role, Scherer, currently executive vice-president and head of Airbus Group International, will run the Toulouse-based firm for a four-year period.
He started his role at Airbus in 1984 and has held a number of positions, including head of marketing and sales in its defence and space division. ATR also confirmed that Giovanni Tramparulo, its current chief financial officer, will remain in his role for a further four years.