The 32-year-old saw off competition from the likes of Juventus forward Cristiano Ronaldo and Liverpool defender Virgil van Dijk to win the prestigious accolade, which is voted for by journalists.
Messi won the award for the first time in 2009 but had not won it since 2015. The Barcelona forward now has one more title than arch rival Ronaldo.
Many had tipped Van Dijk to become the first defender in 13 years to win the coveted title, following in the footsteps of 2006 winner Fabio Cannavaro.
The Dutchman had already been crowned UEFA Player of the Year after winning the Champions League with Liverpool last season.