It was the record fourth consecutive year that Messi was selected player of the year. He was second in the voting in 2007 and '08.
Cristiano Ronaldo, who played for Real Madrid and Portugal, came in second to Messi. It was the fourth time since 2007 Ronaldo was second in the Ballon d'Or balloting. Andres Iniesta, from Barcelona and Spain, was third. He was second a year ago.
Messi set a calendar-year record with 91 total goals last year for Barcelona as a professional player and the Argentine national team.
"To tell the truth, this is really quite unbelievable," Messi said at the announcement ceremony. "The fourth award that I have had is just too great for words.
"I would like to thank my other colleagues from Barcelona. Iniesta, it has been great to train and play alongside you. I would also like to recognize all my friends from the Argentinean national team."
U.S. player Abby Wambach won the FIFA Women's World Player of the Year award with her teammate Alex Morgan, the runner-up. Brazil's Marta, who has won the honor five times and been second twice, came in third for 2012.
The FIFA Men's Coach of the Year was Vicente del Bosque, who leads the Spanish national men's team. The FIFA Women's Coach of the Year was Pia Sundhage who recently resigned as coach of the U.S. women's team. Both the Spanish men and the U.S. women are ranked No. 1 in the world.