The Argentinian won the vote at the ceremony in Milan on Monday night ahead of Juventus superstar Cristiano Ronaldo and Liverpool defender Virgil Van Dijk.
Meanwhile, Megan Rapinoe was rewarded at the FIFA Best awards for leading the United States to the women's World Cup title in July, as was Jill Ellis who won the women's coach award.
USA co-captain Megan Rapinoe won the women's top award after helping her country to the World Cup title this year in a tournament considered to be a milestone in the development and expansion of women's football internationally.
The German's position is exceptionally secure, though, after he led Liverpool to Champions League glory last term and subsequently collected The Best FIFA Men's Coach award this week.
Meanwhile, FIFA said votes from Egypt for Liverpool forward Mohamed Salah did not count because signatures on the ballot "were in capital letters and thus seemed not valid (not authentic)", and "voting forms were also not signed by the (federation) general secretary which is mandatory".
Now there is doubt and questions are being asked over the legitimacy of the voting with countries claiming they didn't vote for Lionel Messi.
Saudi Arabia to restore full oil output by next week
"But first we need to know who and why they acted like that", Mr Le Drian said, adding that the Houthi claims lacked credibility. Iran denies being responsible and has warned any retaliatory attack targeting it will result in an "all-out war".
"That's just the case and as players you can't compare me and Messi because it's totally different", goal.com quoted Van Dijk as saying.
Sudan manager Zdravko Lugarisic and Nicaragua captain Juan Barrera are both listed on the official document as having selected Lionel Messi as their first choice, but according to the Express, both men have disputed this.
"If you ask who should follow me, I'd say Stevie".
Liverpool's Juergen Klopp was voted men's coach of the year while USA national team coach Jill Ellis took home the best women's coach trophy.
NB: Excerpts of this article curled from Daily Mail.
In FIFA's voting breakdown, though, votes for Messi, Sadio Mane in second and Ronaldo in third place were registered for the surprised Barrera.