Real Madrid and Portugal forward Ronaldo, 31, beat Barcelona's Lionel Messi and Atletico Madrid's Antoine Griezmann to the prize.
Ronaldo also won the Ballon d'Or in December, with both honours recognition for success in the Champions League with Real and Euro 2016 with Portugal.
Carli Lloyd of the United States was named the world's best female player.
Leicester's Claudio Ranieri was named best men's coach, ex-Germany boss Silvia Neid won the female coach award, while Penang's Mohd Faiz Subri received the Puskas award for the best goal of 2016.
Hold on... haven't we already had the Ballon d'Or?
We have - but this is different.
For the past six years, the world's best player has received the Fifa Ballon d'Or award.
A version of that prize has been awarded by France Football magazine since 1956, but last year world football's governing body ended its association with that honour.
Instead, it introduced the Best Fifa Football Awards, with Ronaldo the first recipient of its main prize.
Voting for the player and coach categories was by national team captains and managers, selected journalists and, for the first time, an online poll of fans.
Each counted for 25% of the points.
2016 was quite a year for Ronaldo.
As well as scoring the decisive penalty in the shootout to win the Champions League, rescuing Real with a hat-trick in the final of the Club World Cup, captaining Portugal to Euro 2016 glory and being recognised with a fourth Ballon d'Or, he now has something Messi does not - the honour of being named best Fifa men's player.
The former Manchester United forward had been the favourite for the award, following a year in which he continued to deliver remarkable statistics. These included:
44 games, 42 goals, 14 assists.
The third best minutes-per-goal rate (83.68) of anyone scoring a minimum of 10 goals across Europe's top five leagues during 2016, behind Luis Suarez (82.57) and Radamel Falcao (59.6).
Finishing top scorer in the Champions League in 2015-16 with 16 goals, seven more than second-placed Robert Lewandowski.
"As I have mentioned many times, 2016 was a dream year," said Ronaldo. "Real Madrid won the Champions League and the national team won the European Championship."
Fifpro World XI
Despite being on the shortlist for best individual player, Griezmann did not make the best XI.
The line-up features five players from Real Madrid, four from Barcelona, one from Juventus (Dani Alves, who was at Barca for the first half of 2016) and one, Manuel Neuer, from Bayern Munich.
That means no Premier League players were included.