The 32-year-old saw off stiff competition from Juventus' Cristiano Ronaldo and Liverpool’s Virgil van Dijk to win the accolade for the first time after it was split from Ballon d'Or and re-branded in 2016.
Coming second in the year 2016 and 2017, behind Ronaldo, Messi has now beaten his regular competitor to the honour.
Finishing as Europe’s top goalscorer and helping Barcelona retain their La Liga title were enough for Messi to claim the biggest award of the night.
With Messi winning his maiden FIFA Men’s Best Player of the Year means the Argentine talisman has six FIFA awards to his name overall.
Despite winning the highly-rated award, Messi was beaten to the Puskas Award by 18-year-old Daniel Zsori with his 93rd-minute overhead kick for Debrecen against Ferencvaros.
Other personalities, who were also recognised were Barcelona's new boy Frenkie de Jong who, was named in the FIFPro Men’s World XI of 2019 as Jurgen Klopp also won the best men’s coach award.
Liverpool goalkeeper Alisson Becker also took top goalkeeper ahead of Ederson and Marc-Andre ter Stegen.