The left-back joins the Toffees on a three-year contract which will keep him at Goodison Park until 2023, having seen his previous deal with Marseille expire at the end of June.
Nkounkou, 19, did not make a single first-team appearance for the Ligue 1 outfit, spending last season in their 'B' team.
"Niels is a young, talented player with good technical and physical skills. We have been following him for months," Everton director of football Marcel Brands told the club's official website.
"Hopefully he can learn a lot from Lucas Digne and Leighton Baines, as well as Carlo Ancelotti and David Unsworth, and follow the same pathway into the first team the likes of Dominic Calvert-Lewin and Mason Holgate have taken in recent years."
Nkounkou, who has made two appearances for France's Under-19 team, had previously been linked with a move to Juventus.