Eto`o beat Nigeria midfielder Jay Jay Okocha and Ivory Coast striker Didier Drogba to the award.
He follows compatriots Roger Milla, Thomas N`Kono, Jean-Manga Onguene, Theophile Abega and Patrick Mboma in taking African football`s top individual prize.
Orlando Pirates and South Africa striker Lesley Manyathela, who died in a car accident last year, was posthumously given the Goal of the Year, with his mother collecting the award.
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The list of major winners at Caf`s 2003 African football awards:
Footballer of the Year: Samuel Eto`o (Real Mallorca, Spain and Cameroon)
Young Player of the Year: Obafemi Martins (Inter Milan, Italy and Nigeria)
Coach of the Year: Kadiri Ikhana (Enyimba, Nigeria)
Club of the Year: Enyimba (Nigeria)
Team of the Year: Cameroon
Best African Champions League player: Dramane Traore (Ismaili, Egypt)
Goalkeeper of the Year: Idriss Carlos Kameni (Le Havre, France and Cameroon)
Best televised goal of the year: Lesley Manyathela (Orlando Pirates, South Africa).