One of Whitford's most memorable roles was as the evil businessman Eric Gordon in the 1995 comedy Billy Madison. He made his Broadway theatre debut playing Lt. Daniel Kaffee, succeeding Tom Hulce, in A Few Good Men. Whitford also made a guest appearance on ER in the Emmy award-winning March 1995 episode "Love's Labor Lost".

Whitford joined The West Wing as Josh Lyman with the show's premiere in 1999. For his role, he won an Emmy Award in 2001 for Best Supporting Actor in a Drama Series. Whitford also wrote two episodes of the series ("Faith Based Initiative" in the sixth season and "Internal Displacement" in the seventh).

After The West Wing ended in May 2006, Whitford appeared in West Wing creator Aaron Sorkin's later series Studio 60 on the Sunset Strip playing the role of Danny Tripp. He also appeared in the British drama Burn Up on the BBC in July 2008.

He starred on Broadway in Boeing-Boeing which began previews April 19, 2008 and opened on May 4, 2008. Whitford left the show in September of that year and was replaced by Greg Germann.

Whitford is cast in the Joss Whedon/Drew Goddard horror The Cabin in the Woods, set to premiere in 2011.

Whitford is now starring as Dan Stark in the Fox police buddy-comedy The Good Guys, which premiered May 19, 2010. The show also stars Colin Hanks, Jenny Wade and Diana Maria Riva.

Whitford was born in Madison, Wisconsin and graduated from Madison East High School. He majored in English and Theater at Wesleyan University, where his roommate was the younger brother of future castmate Richard Schiff. He went on to receive a fine arts degree from The Juilliard School.

Whitford was married to fellow Wisconsin native, actress Jane Kaczmarek, best known for her role as Lois on Malcolm in the Middle. They lived in San Marino, California with their three children Frances Genevieve (b. January 1997), George Edward (b. December 23, 1999) and Mary Louisa (b. November 25, 2002). On June 19, 2009, the couple announced that they were filing for divorce after 16 years of marriage. One of the last times they were seen together publicly was in September 2008, at the opening of a Los Angeles production of The House of Blue Leaves, in which Kaczmarek was starring. According to a June 2009 magazine interview with More.com conducted prior to announcement of the divorce, she replied "That's a big no comment" when asked to sum up her love life. She also added that she used to believe that she could "“go it alone and as long as I had some fabulous boy on my arm, or man, and my career was sailing, that’s all I needed" whereas she now had grown to appreciate the support of her girlfriends to "to talk about kids, to talk about marriages, to talk about just life."

Whitford is politically liberal and has appeared several times on Real Time with Bill Maher. He once co-hosted The Majority Report on Air America Radio alongside Janeane Garofalo, and made an appearance on the Al Franken Show Party Album.

In May 2007, Whitford was honored by Alliance for Justice, a nonprofit organization, as the 2007 Champion of Justice. He was the keynote speaker for Class Day at Princeton University in June 2007.