The Real Madrid forward received 43.16 per cent of the total votes and was presented with the 2017 award by Diego Maradona and former Brazil striker Ronaldo at the London ceremony after beating off competition from Messi and the world's most expensive player, Neymar.
The men's and women's player and coach awards were decided by a two-part process in a 50-50 split.The captains and head coaches of all the world's national teams count for 50 per cent of the result and the other 50 per cent was made up of votes from 200 football journalists and an online public ballot.
FIFA introduced the 'Best Football Awards' last season after splitting with France Football magazine, which meant they had to end their association with the Ballon d'Or award.
Messi and Ronaldo did not vote for each other in any of their three nominations for the award.
"Thank you a lot, to the guys who voted for me," Ronaldo said. "Real supporters, my team-mates, my coach, my president, I have to thank them too.
"We are in England for the first time and I win consecutive awards. This is a great moment for me. I know I have fans all over the world so thanks a lot for the support."
Cristiano Ronaldo: 43.16% Lionel Messi: 19.25% Neymar: 6.97%
Zinedine Zidane (46.22 per cent of votes) made it a double swoop for Real Madrid after beating off Chelsea's title-winning manager Antonio Conte (11.62 per cent) and Juventus' Massimiliano Allegri (8.78 per cent) to be named Best FIFA Men's Coach.
Zidane became the first coach to win back-to-back Champions League titles and led Real Madrid to their first La Liga title in five years.