The Chelsea marksman beat off competition from Cameroon's three-time winner Samuel Eto'o and Ghana midfielder Michael Essien.
"Drogba was named the Glo-CAF Player of the Year 2009 at the Awards Gala held on Thursday, March 11, at the Banquet Hall, State in Accra, Ghana," CAF said in a statement on their website.
"It served a grand birthday present for Drogba whose 32nd birthday coincided with the ceremony that seeks to reward the finest footballers, officials and administrators for their contribution to the development of the game."
It is the second time for Drogba to win the award, having clinched it in 2006.
The prolific striker scored five goals in the World Cup qualifiers to help Ivory Coast book a place in the 2010 finals in South Africa.
He was also on target for Chelsea as they won the FA Cup final at the expense of Everton.
Algeria, who reached the World Cup for the first time since 1986 after beating Egypt in a playoff, were named the national team of the year.
Mazembe of DR Congo won the best club award after winning the African Champions League.
AC Milan striker Dominic Adiyiah, who played a key role in helping Ghana claim the U-20 World Cup title in Egypt in October, scooped the Young Player of the Year award.