Ganji, who spent the last six years in jail for his critical articles, was awarded the prize for his fight for freedom of expression and his refusal to be silenced.
The award was presented at the opening of WAN's annual congress in Moscow, which is being attended by more than 1,700 newspaper executives and editors.
Ganji dedicated the award to all Iranian dissidents and freedom fighters.
WAN has awarded the Golden Pen annually since 1961.