The former Cameroon international has promised a series of reforms after receiving 43 votes from members of the FECAFOOT general assembly.
Eto’o has enjoyed a brilliant club career, playing for the likes of Barcelona, Inter Milan and Chelsea, while also making over 50 appearances for the Cameroon national team.
At his peak, Eto’o was considered one of the best strikers in the world and he inspired his country to win two Africa Cup of Nations titles and a medal. Olympic gold medal.
“I will remember this day as one of the proudest moments of my life,” Eto’o tweeted on Saturday.
“Each 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 take charge of the federation when Cameroon hosts the Africa Cup of Nations next year, with matches set to begin on January 9.
Africa’s best player four times beat rival Seidou Mbombo Njoya in the vote.