The former Cameroon striker, who lifted the Champions League with Barcelona and Inter Milan, won the election with 43 votes from members of FECAFOOT’s general assembly.
Outgoing president Seidou Mbombo Njoya, who is also a Confederation of African Football vice president, got 31 votes.
Eto’o, 40, will take over an organisation long tainted by infighting, mismanagement and allegations of corruption.
Soccer’s global governing body FIFA has intervened several times to end bickering among FECAFOOT officials
Eto’o had initially been disqualified from running because he is also a Spanish citizen, but the ruling that nobody with dual nationality could run for office was challenged and later tossed out.
He received widespread support from many former team mates in a high profile campaign during which he pledged to rid the game in Cameroon of corruption.
Cameroon will host the African Cup of Nations from Jan. 9 to Feb. 6. It was stripped of the right to host the tournament in 2019 because of delays in preparation and security concerns.
Eto’o won the tournament twice with the Indomitable Lions during his playing days.
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