From the mid-1990s (while at Northwestern University) through 2001, Dudek appeared in various theater productions and on Broadway. She made her Broadway debut in Wrong Mountain in 2000. She won the Connecticut Critics Circle Award for outstanding performance in The Glass Menagerie. After success on Broadway, she made the jump to television. Her first starring role on television came when she was cast as the lead in the British comedy drama The Book Group. The show aired on Channel 4 in the United Kingdom to rave reviews. In her native United States, Dudek has since guest starred on other TV shows, including Desperate Housewives (as Karl Mayer's girlfriend in Season 1), How I Met Your Mother (as Ted's Krav Maga-trained ex-girlfriend), Friends (as 'Precious', Mike Hannigan's girlfriend), ER (as a mother who accidentally shot her son), Charmed, Bones (as Seeley Booth's lawyer girlfriend), Numb3rs, and Six Feet Under. She also played Lucinda Barry in the pilot episode of Psych, and a teacher who has a sexual relationship with one of her students (based on the case of Debra Lafave) on Law & Order: Criminal Intent. In both "Friends" and "How I Met Your Mother", her character was dumped on her birthday.
Dudek had a recurring role on House (from season 4 onwards) as Dr. Amber Volakis, one of 40 physicians under consideration by Dr. Gregory House for permanent positions on his team. Her character, nicknamed "Cutthroat Bitch" by House, continued to the end of season 4 but was killed off in the two-part season finale, "House's Head" and "Wilson's Heart". She would later reappear as a hallucination by House in the season 5 episode "Saviors", appearing in this form for the remainder of the season. Dudek later appeared in Mad Men as next-door neighbor Francine Hanson, and on Big Love as one of antagonist Alby Grant's wives, both recurring roles. In 2010, she joined the cast of Covert Affairs. She played Anthony Hopkins' character's daughter in the 2003 film The Human Stain, and cruise line heir Tiffany Wilson in the 2004 comedy film White Chicks. In 2012, she played an ISS astronaut in one episode of the TV show Touch. She also reprised her role as Amber Volakis for the House series finale "Everybody Dies".