The Inter Miami forward was presented with the award by former England captain David Beckham at a ceremony in Paris.
Messi's win stems largely from his performances at the 2022 FIFA World Cup in Qatar, where he captained Argentina to glory.
The 36-year-old also won the French Ligue 1 title with Paris Saint Germain last season before moving to America's Major League Soccer.
“I couldn’t imagine having the career that I’ve had,” Messi said.
“Everything that I’ve achieved. The fortune I’ve had playing for the best team in the world, the best team in history. It’s nice to win these individual trophies. To win the Copa America and then the World Cup, to get it done is amazing.”
Manchester City forward Erling Haaland and PSG striker Kylian Mbappe came second and third respectively.
Messi tipped the two goals machines to follow in his footsteps one day.
"Haaland and Mbappe will win the Ballon d’Or one day," Messi said in his acceptance speech.
"Erling deserved it very much too, he has won the Premier League, and Champions League while being the top scorer of everything. This award could have been yours today too. I’m sure in the next years you will win it."
