She gained wider recognition in the late 2000s for portraying the FBI Supervisory Special Agent Emily Prentiss on the CBS crime drama series Criminal Minds.

Her character handled the case against SVU commanding officer Captain Donald Cragen (Dann Florek), suspected of murder after awakening next to a dead woman in the 13th-season finale.

[15][16][17] Brewster was a regular on The Thrilling Adventure Hour, a staged production in the style of old-time radio that was recorded monthly at Largo in Los Angeles.

She played the recurring character of Sadie Doyle, the alcoholic socialite who can communicate with the supernatural alongside her husband, Frank (Paul F. Tompkins), in the "Beyond Belief" segments.

In early April 2013, Brewster appeared in Modern Family as Trish in episode 20, "Flip Flop", playing an art expert who is dating Gloria's ex-husband, Javier.

In August 2016, it was announced that she would be reprising her role as Emily Prentiss on Criminal Minds and would once again be a series regular after co-star Thomas Gibson was fired by CBS over an on-set altercation.

On the March 30, 2006, episode of Late Night with Conan O'Brien, Brewster revealed that she had received a handwritten note indicating Hugh Hefner would like her to pose for Playboy.