Malkovich, 60, received the award from German actress Vernica Ferres at a ceremony on Saturday at the Zurich opera house.
The two-time Oscar nominated movie star was awarded for his life’s work, including his roles in such films as Dangerous Liaisons and Being John Malkovich.
He also presented Cut Bank, the latest film in which he stars, a thriller which was given a special screening at the festival.
In an interview with 20 Minuten, Malkovich, who has shaved his head and grown a goatee beard, rejected the idea he was an eccentric artist, saying he was “the least eccentric person I know”.
He told the newspaper he does not see himself a s humble person but he is “less arrogant” than when he was 26.
About receiving the Golden Eye, he said it was a “beautiful thing” when other people recognized your work.
Diane Keaton, another Hollywood star, was earlier honoured during the 10-day festival.
Keaton, famous for her role in Woody Allen’s 1977 film Annie Hall, for which she won an Oscar, has starred in more than 60 feature films.
The festival screened a retrospective of six films featuring the 68-year-old actress, who was awarded the “Golden Icon” award.
The festival also honoured film music composer Hans Zimmer (The Lion King, Rain Man, As Good as it Gets) with a lifetime achievement award.