The 40-year-old beat incumbent Seidou Mbombo Njoya to the position after five other candidates pulled out on the morning of the election on Saturday.
Eto’o garnered 43 votes while Mbombo Njoya, who is also the Confederation of African Football’s fourth vice president, received 31 votes.
"We have to bring footballers to the centre of our policies," Eto’o said afterwards. "It is our role to ensure that those who play this discipline make a decent living out of it."
Speaking prior to the elections, the three-time UEFA Champions League winner, who has promised a massive improvement in infrastructure, said: "I've spoken to the business community and we're certain we'll get the right investors who can accompany us in fulfilling our goals."
Eto’o retired from football in September 2019 and turned out for clubs including Real Madrid, Barcelona, Inter Milan and Chelsea during an illustrious career, and is also the all-time top scorer in Africa Cup of Nations history with 18 goals.
The four-time African footballer of the year won 118 caps for Cameroon, scoring 56 goals and claimed the African Cup of Nations on two occasions.
Cameroon are due to host the next edition of the African Cup early next year.
