Kroos: Neuer's third place in Ballon d'Or unfair
Ronaldo claimed the award for a third time on Monday, finishing as the clear winner with 37.66 per cent of the vote.
His La Liga rival Messi took second with 15.76 per cent, while Bayern Munich goalkeeper Neuer was third, just 0.04 per cent behind the Barcelona man.
Having clinched a domestic double with Bayern in 2014, Neuer was a key member of Germany's World Cup-winning side in Brazil, and his former club team-mate Kroos believes the keeper deserved to at least take second spot ahead of Messi.
"It was surprising and a little unfair that Neuer finished behind Messi," he told Sky Sports News.
"I thought it would be close between Manuel and Cristiano.
"Manuel was the best goalkeeper by a long way and Cristiano the best outfield player.
"It was between the two of them really. Manuel would have been a worthy winner but Cristiano also deserved it."