The 23-year-old Republic of Ireland defender made 27 appearances for the Ligue 1 side last season.
He becomes Everton’s fifth summer signing after midfielder Tim Iroegbunam, forwards Iliman Ndiaye and Jesper Lindstrom and the return of Jack Harrison on loan from Leeds.
“I’m buzzing and so happy to have signed for Everton,” O’Brien said.
“I’ve been dreaming of this kind of move in the Premier League, with such a historic club. It’s a very exciting move for me.
“Everton is a huge club with a lot of history behind it and there’s a big future as well.
“When the transfer window opened there were other clubs in for me but there was only one club I wanted to go to – it was Everton.
“They’ve shown the faith in me so now it’s my turn to show why on the pitch.”
O’Brien began his career with hometown club Cork City and then joined Crystal Palace’s academy on loan before signing for the Premier League club permanently.
After loan spells with Swindon Town and Belgian club RWD Molenbeek, he joined Lyon for an undisclosed fee last summer.
The defender says Everton boss Sean Dyche’s development of youth, including fellow centre-back Jarrad Branthwaite, is what attracted him to the club.
Dyche added: “Jake further strengthens our talented core of centre-backs and adds competition to our squad which can help us continue to progress.
“He is still young but has earned valuable experience both abroad and at international level, and has many impressive attributes to become a top-quality player for Everton in the Premier League.”
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