The 28-year-old Argentine had 41.33% of the vote, with Real Madrid forward Cristiano Ronaldo (27.76%) second and Barca's Neymar (7.86%) third.
Either Messi or Ronaldo, who became a three-time winner last year, have won the past eight awards.
United States midfielder Carli Lloyd, who scored a hat-trick in the World Cup final, won the women's award.
England coach Mark Sampson was beaten to the women's football coach of the year award by USA boss Jill Ellis.
Barcelona coach Luis Enrique won the world coach of the year award after leading his side to five of the six trophies on offer in 2015, including the Champions League, La Liga and the Copa del Rey.