The 22-year-old won the award for the first time, easily beating the last two winners - Cristiano Ronaldo and Kaka, his two Barcelona clubmates Andres Iniesta and Xavi in voting among national team captains and coaches. Messi received 1,047 points in voting. Ronaldo was second with 352 points, followed by Xavi with 196 points.
It is a perfect year for the winger, who won an unprecedented treble of the Primera Liga, Champions League, Copa del Rey and received the Ballon D'Or as the best player in Europe.
Messi said: "I'm extremely happy. We've just ended a historic year, a perfect year in which we've won every competition we've played in. We just needed to take this last step and everything has worked out how we wanted. It's amazing."
FIFA Player of the Year list
2009 - Lionel Messi, Argentina
2008 - Cristiano Ronaldo, Portugal
2007 - Kaka, Brazil
2006 - Fabio Cannavaro, Italy
2005 - Ronaldinho, Brazil
2004 - Ronaldinho, Brazil
2003 - Zinedine Zidane, France
2002 - Ronaldo, Brazil
2001 - Luis Figo, Portugal
2000 - Zinedine Zidane, France
1999 - Rivaldo, Brazil
1998 - Zinedine Zidane, France
1997 - Ronaldo, Brazil
1996 - Ronaldo, Brazil
1995 - George Weah, Liberia
1994 - Romario, Brazil
1993 - Roberto Baggio, Italy
1992 - Marco Van Basten, Netherlands
1991 - Lothar Matthaus, Germany
Real Madrid's Cristiano Ronaldo won the FIFA Puskas award for the best goal of the 2008/09 season - his long-range thunderbolt for former club Manchester United against Porto in the Champions League in April.
The FIFA Fair Play Award was given posthumously to Sir Bobby Robson for his "outstanding commitment to the values of fair play throughout his career". The award was collected by his widow Elsie.
Lastly, the FIFA/FIFPro World XI, voted for by members of the international professional footballers' union FIFPro, were:
Goalkeeper: Iker Casillas (Real Madrid)
Defenders: John Terry (Chelsea), Nemanja Vidic (Man Utd), Patrice Evra (Man Utd), Daniel Alves (Barcelona)
Midfielders: Xavi (Barcelona), Andres Iniesta (Barcelona), Steven Gerrard (Liverpool),
Attacks: Lionel Messi (Barcelona), Cristiano Ronaldo (Real Madrid), Fernando Torres (Liverpool).
