Ronaldo led his country to their first major title at the European Championship last summer.
The 32 year old player was injured in the final against hosts France but barked instructions from the sidelines as Eder netted the extra-time winner for Portugal.
“It was a very special year for me because the Euros was the only trophy I was still missing,” Ronaldo said.
“I want to thank my team-mates from Real Madrid and the Seleção, the coach and the staff, and all the Portuguese who were very important in winning the European Championship and made us believe that teams that are not favorites can also win.”
The prolific attacker previously won the Ballon d’Or and FIFA’s The Best award to cap a sublime 2016.
Bayern Munich youngster Renato Sanches was voted young player of the year, while national team coach Fernando Santos lifted the coach of the year award
Portugal have a World Cup qualifier against Hungary on Thursday before taking on Sweden in a friendly three days later.