The Real Madrid and Croatia midfielder starred for both club and country as Madrid won a third straight Champions League, and he inspired Croatia to reach the World Cup final for the first time.
"The emotion is huge because it is thanks to the work of everyone. So many people have come together and so many have supported me," said Modric.
Modric beat out Liverpool's Egyptian forward Mohamed Salah and Ronaldo, who along with Messi did not attend the glitzy awards ceremony in London.
Both are in action for Juventus and Barcelona on Wednesday, but their no-show attracted criticism after so many years on top.
"Everyone has their own reasons," said Modric. "Obviously I would have liked them to be here but they aren't."
Salah did not go away empty-handed, however, as he picked up the Puskas award for best goal for his strike against Everton in the Merseyside derby last December.
Modric was joined by Real teammates Sergio Ramos, Raphael Varane and Marcelo in the FIFPro team of the year, also featuring David De Gea, Dani Alves, N'Golo Kante, Eden Hazard, Kylian Mbappe, Messi and Ronaldo.
France's World Cup-winning coach Didier Deschamps won the best coach of the year prize in recognition for his work in leading Les Bleus to success in Russia.
Thibaut Courtois won the best goalkeeper award for helping Belgium reach the World Cup semi-finals as well as the FA Cup with Chelsea before a summer move to Madrid.
Brazil's Marta was crowned best women's player for a record sixth time for her role in winning the Copa America to beat out Lyon duo Ada Hegerberg and Dzsenifer Marozsan.
Lyon boss Reynald Pedros did win the award for best women's coach, though, after winning the Champions League with the French giants.
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