Huffman is known for her roles in Desperate Housewives and Transamerica. On television, she starred as Dana Whitaker in the dramedy Sports Night, and has had guest starring roles on Frasier, The X-Files, The West Wing and Studio 60 on the Sunset Strip. In 2001 she appeared in the made for TV movie Snap Decision with Mare Winningham. Huffman has appeared in films such as Raising Helen and Christmas with the Kranks. In 2003 she starred in Showtime's dramedy Out of Order. Huffman won an Emmy for her work on Desperate Housewives (Outstanding Actress in a Comedy Series), as well as two 2005 Screen Actors Guild Awards (Best Actress - Comedy Series and part of Best Ensemble - Comedy Series). Huffman's performance in the film Transamerica was praised by many critics and garnered her a Golden Globe Award for Best Actress as well as nominations for the Best Actress (Screen Actors Guild) and Best Actress (Academy Awards). Huffman is now a voting member of the Academy of Motion Picture Arts and Sciences.

Huffman is also the co-author of the self-help book, A Practical Handbook for the Boyfriend. She is the only actress to have appeared in all three television shows created by Aaron Sorkin (Sports Night, The West Wing, and Studio 60 on the Sunset Strip). On June 23, 2008, the Hollywood Chamber of Commerce announced Huffman and her husband William H. Macy will each receive a star on the Hollywood Walk of Fame in the upcoming year.

Huffman is married to actor William H. Macy, with whom she has two daughters Sofia Grace (born August 1, 2000) and Georgia Grace (born March 14, 2002). They married on September 6, 1997. She has appeared on television, in movies, and on stage many times with her husband, such as on the TV show Sports Night and in the movie Magnolia. The couple have become the subject of a running gag on the satirical news show The Colbert Report, in which the couple (who live a quiet life outside the media spotlight) are regularly referenced as representing the greatest of today's celebrity couples in a culture obsessed with celebs. Colbert refers to the couple as "Filliam H. Muffman", a play on the current trend by media types to combine the names of major celebrity couples, in the mold of "Bennifer", "Brangelina" and "TomKat." In 2005, Huffman revealed that she had suffered from both anorexia and bulimia in her late teens and twenties. At the height of her bulimia she would purge up to six times a day. Her weight dropped to 98 lbs, her periods stopped, and she was too weak to go jogging. However, with therapy and upon meeting Macy she managed to overcome those conditions. She is still known for her self-deprecating humor and her belief that she is "not pretty." She is a huge fan of Tina Turner and her dream was to be a back-up singer, so when Huffman was on The Oprah Winfrey Show, Winfrey surprised her with a visit from Tina Turner where the two got to sing together.

• The Politician's Wife (2010) (in production)
• Come Back to Sorrento (2009) (pre-production)
• "Desperate Housewives" .... Lynette Scavo (110 episodes, 2004-2008)
       - A Vision's Just a Vision (2008) TV episode .... Lynette Scavo
       - Me and My Town (2008) TV episode .... Lynette Scavo
       - City on Fire (2008) TV episode .... Lynette Scavo
       - What More Do I Need? (2008) TV episode .... Lynette Scavo
       - There's Always a Woman (2008) TV episode .... Lynette Scavo
        (105 more)
• Phoebe in Wonderland (2008) .... Hillary Lichten
• Georgia Rule (2007) .... Lilly
• Choose Your Own Adventure: The Abominable Snowman (2006) (V) (voice) .... Pilot Nima
• Transamerica (2005) .... Bree
• Christmas with the Kranks (2004) .... Merry
• Reversible Errors (2004) (TV) .... Gillian Sullivan
  ... aka Scott Turow's Reversible Errors (USA: complete title)
• Raising Helen (2004) .... Lindsay Davis
• "The D.A." .... Charlotte Ellis (3 episodes, 2004)
       - The People vs. Achmed Abbas (2004) TV episode .... Charlotte Ellis
       - The People vs. Oliver C. Handley (2004) TV episode .... Charlotte Ellis
       - The People vs. Patricia Henry (2004) TV episode .... Charlotte Ellis
• "Frasier" .... Julia Wilcox (8 episodes, 2003)
       - A Man, a Plan and a Gal: Julia (2003) TV episode .... Julia Wilcox
       - No Sex Please, We're Skittish (2003) TV episode .... Julia Wilcox
       - A New Position for Roz (2003) TV episode .... Julia Wilcox
       - Analyzed Kiss (2003) TV episode .... Julia Wilcox
       - Farewell, Nervosa (2003) TV episode .... Julia Wilcox
        (3 more)
• "Kim Possible" .... Doctor Director / ... (2 episodes, 2002-2003)
  ... aka Disney's Kim Possible (USA: complete title)
       - The Ron Factor (2003) TV episode (voice) .... Dr. Betty Director
       - Number One (2002) TV episode (voice) .... Doctor Director
• "Out of Order" (2003) TV mini-series .... Lorna Colm
• House Hunting (2003) .... Sheila