Messi's Barcelona team-mate Xavi and Real Madrid's Cristiano Ronaldo were also shortlisted with clubs from Spain's La Liga providing the top three for the third year in a row.
Messi, who won the Ballon d'Or in 2009 and 2010, will be the favourite to complete a hat-trick of titles after his man-of-the-match performance helped the Spanish side beat Manchester United in the Champions League final in May.
Portuguese forward Ronaldo won the Ballon d'Or in 2008 while Xavi has finished third in the last two editions.
Former France international and current UEFA President Michel Platini won the Ballon d'Or for three consecutive years from 1983.
Last year, the FIFA Player of the Year and the Ballon d'Or awards merged into the FIFA Ballon d'Or and votes now come from the coaches and captains of international teams as well as from journalists.
The winner will be announced on Jan. 9 in Zurich with 1987 Ballon d'Or winner Ruud Gullit of Netherlands presiding over the ceremony.
FIFA Secretary General Jerome Valcke said the ceremony is likely to be the last in Switzerland for a while.
"We will take the Ballon d'Or out of Zurich. It could be Paris, Barcelona, Madrid or other European cities, but it will stay in Europe," he told reporters at the headquarters of France Football magazine, who co-organise the event.
Manchester United manager Sir Alex Ferguson, Barcelona's Pep Guardiola and Real Madrid's Jose Mourinho were shortlisted for the Coach of the Year award.
Brazil's Marta will be looking for a sixth consecutive Women's Player of the Year award but faces competition from Japan's Homare Sawa and American Abby Wambach.
