The Argentina captain saw off competition from France pair Kylian Mbappe and Karim Benzema to claim the award for a second time at a ceremony held in Paris on Monday night.
The 2022 awards took into consideration performances between August 2021 and December 2022.
In a World Cup year, Messi was the overwhelming favourite for the award after captaining Argentina to their third global title in Qatar.
The Paris Saint Germain star scored seven goals and provided three assists for his teammates and was named player of the tournament.
Upon collecting his Best FIFA award, which he previously won in 2019, Messi said: "Wow, this is amazing. It's been a tremendous year and it's an honour to win this award.
"Without my team-mates, I wouldn't be here. I achieved the dream I had been hoping for so long. Very few people can achieve that and I have been lucky to do so.
"It's the most wonderful thing that's happened to me in my career."
Further wins for Argentina on the night saw Lionel Scaloni win coach of the year while Emiliano Martinez won goalkeeper of the year.
Barcelona striker Robert Lewandowski had won the previous two editions of the award.
Full list of winners:
The Best men's player: Lionel Messi
The Best women's player: Alexia Putellas
The Best men's goalkeeper: Emiliano Martinez
The Best women's goalkeeper: Mary Earps
The Best men's coach: Lionel Scaloni
The Best women's coach: Sarina Wiegman
The Best Puskas award: Marcin Oleksy
The Best fan award: Argentina fans
The Best fair play award: Luka Lochoshvili
