The Confederations Cup champions accrued 840 points in 2005, having started the year as world number one and recorded 10 wins, four draws and two defeats.
The Czech Republic were second, improving on their ranking in 2004 by two places, FIFA said in a statement.
Ghana won the race for the best mover title, beating Ethiopia and Togo.
In an eventful year, the African side qualified for the World Cup finals, to be held in Germany from June 9, for the first time.
Ghana are ranked 50 among the world's teams at the end of year, up from 77th at the end of 2004.
FIFA said 743 matches were contested during 2005, with almost half played as part of preparations for next year's World Cup.
