The 32-year-old will join the Turkish side when the transfer window officially opens, as reported by the club’s official website.
Valbuena spent two years at Lyon, scoring eight goals in 29 league appearances this season.
The former France international has previously played for Dynamo Moscow, Marseille and Libourne.
A diminutive yet direct player, Valbuena created 43 chances in Ligue 1 this campaign, while he also retained possession to excellent effect as he completed 88% of the passes that he attempted.
Fenerbahce finished third in the Turkish Super Lig and will hope that the arrival of Valbuena will improve their fortunes next season.
Despite his ability, Valbuena found it difficult to command a regular starting berth for Lyon in the second half of the season following the arrival of Memphis Depay from Manchester United.
Valbuena should be a regular for Fenerbahce, and will hope to help the club make an impact in the Europa League, which they will enter in the third qualifying round.
Mathieu Valbuena was successful with 58% of his attempted take-ons in Ligue 1 this season.