Although she originally intended to become an optometrist, Farmiga attended Syracuse University's School of Visual and Performing Arts. She made her Broadway debut in 1996 as an understudy in the play Taking Sides. The same year, she starred as Miranda in the American Conservatory Theater production of The Tempest. Throughout the late 1990s, she continued appearing in stage, television and film roles, including a part in the 1998 film Return to Paradise.

Farmiga appeared in several high profile films in the early 2000s, including Autumn in New York and 15 Minutes. She also appeared in the 2004 remake of The Manchurian Candidate. Her lead performance in the 2005 film Down to the Bone received a "Best Actress" award from the Los Angeles Film Critics Association. In 2006 she appeared in Running Scared, and as a police psychiatrist in Martin Scorsese's The Departed.