The federation which is known as Fecafoot is set to hold its presidential elections at its headquarters in Tsinga, Yaounde, Cameroon on Saturday.
Eto'o, who is widely regarded as one of the greatest African footballers of all time, is up against five fellow candidates Jules Denis Onana, Nyamsi Jean Crepin, Seidou Mbombo Njoya (incumbent), Tagouh Justin and Wandja Zacharie.
Bafana's most capped player, Mokoena feels that retired players have what it takes to lead the Football Associations and he tipped the Cameroonian icon to win the elections.
"This is Aaron Mokoena, the former Bafana Bafana captain, I just want to wish you all the best in your elections tomorrow," Mokoena said in a video posted on Football Stage.
"It is about time that we show that we can take our football to another level."
"For me personally, the fact that you have played the game at the highest level I think you deserve to avail yourself, you deserve to be the president of Cameroonian FA."
Mokoena ventured into coaching after retiring from professional football and he has worked for Cape Town City as an assistant coach and he currently runs the Aaron Mokoena Football Academy.
The former Blackburn Rovers defender hopes Eto'o comes out on top in the elections because he believes the four-time African Footballer of the Year can succeed as Fecafoot president.
"I really hope that people in Cameroon will vote for you and they can understand that you can take Cameroonian football to another level," he added.
"I would like to wish you all the best on the behalf of South African people and football lovers. We are all behind you and I hope you will win. All the best brother. Go and do this."
The newly elected Fecafoot president will run football affairs in Cameroon for the next four years. Read Full Story
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