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Nkounkou has agreed a three-year deal with the Merseyside club following the expiration of his contract at Marseille.
The 19-year-old played 14 times for Marseille's B team in National 2 in 2018-19, France's fourth tier, while also being named on the bench for the first team twice.
He was a rumoured target for Serie A champions Juve but will now be working under Carlo Ancelotti at Goodison Park, though Nkounkou will first bolster David Unsworth's Under-23 side.
Everton, who are unbeaten since the resumption of the Premier League, have Lucas Digne – France's first-choice left-back – and Leighton Baines as their options on the left side of their defensive line.
Baines, however, is yet to agree to a contract extension, with the 35-year-old's current deal set to run out at the end of the season. The veteran has been offered a one-year deal by the club's board.
Speaking on the clear potential possessed by the teenager, Everton's director of football, Marcel Brands told the club's official website: “Niels is a young, talented player with good technical and physical skills. We have been following him for months.
“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.”
The news is likely to be music to the ears of head coach Carlo Ancelotti, who recently stated that his young squad should be competing for the Premier League title, no matter how long it takes.
“Everton has to be competitive and fight for the first position of the Premier League with Liverpool, with Chelsea, with Tottenham, with Manchester United, with all the big teams,” the Italian told Sky Sports.
“I don't know how long it will take but I hope that soon we are able to compete. We have a young squad with young players with a lot of skills, a lot of ability. I think just the fact that we can improve this skill and this ability can give us more opportunity to stay at the top.”