He played the best friend of main character Nick Powell in the thriller The Invisible, a remake of a Swedish film, which starred Justin Chatwin and Marcia Gay Harden and was released on April 27, 2007.

Fanboys was shot in spring 2006 in New Mexico, and also stars Sam Huntington, Dan Fogler, Jay Baruchel and Veronica Mars' Kristen Bell.

Whether on purpose or not, Chris frequently appears in movies with a group of actors including Emile Hirsch, Paul Dano, Amanda Seyfried and Nikki Reed.

In Infestation, an action comedy by Kyle Rankin that was shot in summer 2007 in Bulgaria, he plays the lead role—a young man named Cooper who has to fight for survival against giant alien insects that have taken over the world.

Marquette has also been seen as a guest star on several TV shows, such as ER, Touched by an Angel, 7th Heaven, Miracles, Boston Public and Judging Amy.

As Christopher Marquette, he returned on-screen, in late 2010, with fellow Joan of Arcadia actor Michael Welch as two friends who murder together in the Criminal Minds episode entitled "JJ".