The former Cameroon international promised an array of reforms after receiving 43 votes from members of FECAFOOT’s general assembly.
Eto’o enjoyed a glittering club career, playing for the likes of Barcelona, Inter Milan and Chelsea, while also making over 50 appearances for the Cameroon national side.
At his peak, Eto’o was considered one of the best strikers in the world and he inspired his country to win two African Cup of Nations titles and an Olympic gold medal.
“I’ll be remembering today as one of the proudest moments of my life,” Eto’o tweeted on Saturday.
“Every vote represents the energy and ambition of our football family to take our beloved sport to a level we’ve never seen before.”
He will now be in charge of the federation for when Cameroon hosts the African Cup of Nations next year, with games set to begin on January 9.
The four-time African Footballer of the Year beat rival Seidou Mbombo Njoya in the voting.