The current England captain was honoured for his allround display in the Ashes series against Australia last summer.
The first of this award, instituted two years ago, was won by Australian skipper Ricky Ponting, followed by Shane Warne the next year.
''We took soundings from writers and commentators in all the cricketing countries, and there were only two people in it, Flintoff and Warne,'' Wisden editor Matthew Engel told the Times.
''We felt in the end that 2005 was the year when Freddie touched greatness,'' he added.
Apart from this, the magazine also announced its list of five cricketers of the year and three of Freddie's teammates, seamers Matthew Hoggard and Simon Jones and big hitter Kevin Pietersen, found a place in it along with Australians Brett Lee and Ponting.
''The Five have never been the world's top five,'' Engel said.
''The choice is based on their influence on the English season,'' he added.