The 46-year-old will take over from Remi Garde after an impressive four-year spell with Stade de Reims, having signed a two-year dealOlympique Lyonnais coach following the departure of Remi Garde.
Fournier takes over at Stade Gerland after Garde announced that he would not be renewing his contract in order to take a break from football.
The 46-year-old leaves Stade de Reims following a four-year spell in which he guided them back to the French top flight, ending a 33-year absence in 2012.
"OL have finalised the arrival of Hubert Fournier, the former coach of Stade de Reims, who will succeed Remi Garde on the bench of the team," the club confirmed via their official website.
"The 46-year-old coach has signed a two-year contract with the club."
Fournier made 58 appearances for Lyon as a player between 1998 and 2000.
Reims finished 14th in their first season back in Ligue 1 and improved on that showing this term as they ended the campaign in 11th.
Fournier will now look to build on the success he enjoyed at the Stade Auguste Delaune with a Lyon side that came fifth in Ligue 1 in 2013-14, missing out on Champions League football.