The Inverness-born actress will be patron of The Young and the Wild - which will featured specially-programmed screenings, networking events, workshop, on-stage interviews and masterclasses.
The festival has instigated a competition to try to unearth a new young Scottish filmmaker and will be allowing a group of young programmers to present their favourite films at the festival.
The Young and the Wild line-up is being staged as part of Scotland's Year of Young People.
Gillan said: "This builds on the great work the Edinburgh International Film Festival has been doing for the past four years in developing and inspiring young people who have a passion for cinema.
"Through this programme young people will be able to access great international cinema, but more importantly learn from filmmakers from around the world who will visit the festival in June.”
Diane Henderson, deputy artistic director at the festival, said: "To have support from Karen Gillan, one of Scotland’s most treasured and successful actor/writer/directors, is a huge honour for us. Karen is already one of our esteemed Honorary Patrons and to have this additional support from her means a great deal to all of us here at EIFF.”