Emily is a vegan and a committed supporter of animal rights causes. She and her close friend, Melanie Lynskey, are members of PETA. Emily graduated from Boston University's Professional Actors Training Program with a Bachelor of Fine Arts in Theater.

Deschanel made her feature film debut in 1994's It Could Happen to You. Her next notable role was in Stephen King's Rose Red in 2002. She then appeared in Cold Mountain, The Alamo and Spider-Man 2, and was named one of "six actresses to watch" by Interview Magazine in 2004. After starring in 2005's Boogeyman, Deschanel landed the role of Dr. Temperance Brennan on FOX's Bones, a series based on the heroine in the novels of real-life forensic anthropologist Kathy Reichs. She received a 2006 Satellite Award nomination and a 2007 Teen Choice Award nomination for her performance, and has served as co-producer since the start of the show's third season.