Messi, who won the Spanish La Liga title with Barcelona last season as well as the European golden boot having scored 54 goals in 58 games in all competitions, last won the award in 2015.
He suffered an injury at the beginning of the season, but he is back to his good form and has been decisive for Barcelona this season.
Lionel Messi did not however, enjoy success with the national team, losing in the Copa America semi-finals to rivals Brazil.
Messi’s win also marks a return to the dominance of the Argentine and Ronaldo, who between them have won the award all but once since 2007.
The monopoly of Lionel Messi and Cristiano Ronaldo in winning the Ballon d'Or was broken last year when Croat Luka Modric beat them to the award.