Messi won the trophy ahead of Barcelona teammates, Xavi Hernandez and Andres Iniesta.
He was voted on by the coaches and captains of national teams plus invited journalists.
The 23-year-old forward helped an exciting Barcelona team retain its Spanish league title and lead the standings again this season.
Messi also won the award last year.
Barcelona has now provided eight winners in the 20-year history of the FIFA honour.
Jose Mourinho was selected FIFA’s 2010 men’s soccer coach of the year after leading Inter Milan to the European Champions League title.
Mourinho, the self-dubbed “Special One,” beat Vicente del Bosque of World Cup champion, Spain and Pep Guardiola of Spanish champion, Barcelona, in the inaugural prize, announced during the FIFA player of the year ceremony.
The Portuguese coach also led Inter to the Italian league and cup double before leaving to join Real Madrid.
The award was voted on by national teams coaches and captains plus selected reporters.
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