Weetalknaija.com.ng reports that Eto’o, who polled 43 votes, defeated the incumbent president, Seidou Mbombo Njoya, who scored 31 votes.
Eto’o was acting as the global ambassador for the Qatar 2022 World Cup while Njoya is currently the fourth vice-president of the Confederation of African Football.
Seven candidates had planned to contest the elections, but five of them pulled out on the morning of the elections.
Among those giving up their candidacy on Saturday morning were former Cameroon internationals Maboang Kesack and Jules Denis Onana.
Prior to the election, the former Cameroon international had also promised to construct at least 10 stadiums during his mandate.
“We have to bring footballers to the centre of our policies. It is our role to ensure that those who play this discipline make a decent living out of it.
“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,” he had said.
He will now be head of Cameroon’s FA (Fecafoot) when the country hosts the Africa Cup of Nations in January and February.
The 40-year-old won the continental title twice with the Indomitable Lions in 2000 and 2002, and he is celebrated as one of the icons of Cameroon football after claiming the African Player of the Year award for a record four times (2003, 2004, 2005 and 2010).