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.
