Laurent Mekies joined F1's governing body as Safety Director in 2014 and took on the role of Deputy Race Director, reporting to Race Director Charlie Whiting, when Herbie Blash stepped away from F1 in 2016.
He was responsible for all safety and medical matters across the FIA’s championships, as well as R&D and homologation on both the track and road and latterly sporting matters.
Mekies will join Ferrari on September 20, serving in their technical team and reporting to Technical Director Mattia Binotto.
The FIA say he will continue to work for the governing body until the end of June in his role as Safety Director but will immediately cease all F1 duties.
Last year rival F1 teams were left frustrated when the FIA's F1 technical director Marcin Budkowski agreed to join Renault, given his experience on the other side of the fence. Budkowski is set to start work later this year.
Last week, the FIA announced former Ferrari Chief Designer Nikolas Tombazis had joined as their new head of single-seater technical matters.