The Barcelona star scored more league goals than anyone else in Europe last season, registering 36 times as he helped the Spanish side win another La Liga title.
It is also the sixth time the 32-year-old has scooped the award, now seeing him move one ahead of rival Cristiano Ronaldo.
The duo have dominated the award since 2008, with their string of victories only interrupted by Luka Modric last year.
It was the second award of the night for the Argentinean forward, who was also included in the men’s team of the 2018-19 season – as voted for by their fellow professionals.
Who did Ronaldo and Messi vote for?
FIFA have revealed the breakdown of the vote, with some interesting surprises among the selections.
Messi went for Liverpool winger Sadio Mane and had Ronaldo as his second pick, but Ronaldo did not return the favour, omitting Messi from his top three while opting for Juventus team-mate Matthijs de Ligt as his first option.
Alisson picked up the individual goalkeeping accolade as well as being selected in the best XI after helping Liverpool to the Champions League title and Brazil win the Copa America.
Matthijs de Ligt (Netherlands, Juventus), Sergio Ramos (Spain, Real Madrid), Virgil van Dijk (Netherlands, Liverpool) and Marcelo (Brazil, Real Madrid) made up the defence.
The midfield featured Luka Modric (Croatia, Real Madrid), Frenkie de Jong (Netherlands, Ajax) and Eden Hazard (Belgium, Real Madrid).
While up front it was Kylian Mbappe (France, Paris Saint-Germain), Lionel Messi (Argentina, Barcelona) and Cristiano Ronaldo (Portugal, Juventus)