After college, Bakkedahl toured for a year with the Repertory Theater of America. After moving to Chicago, he made a name for himself at the Improv Olympic performing in the influential two-man improv show ZUMPF with his teacher Miles Stroth. Dan went on to perform at the Second City mainstage, eventually writing “Doors Open on the Right,” Second City’s 90th Revue. In Chicago, he is often noted for having left the Second City mainstage due to artistic differences.
Bakkedahl continues to perform regularly at comedy venues such as the Upright Citizens Brigade Theatre, Magnet Theater and Second City in Los Angeles.
Bakkedahl's best known television work was on Comedy Central's The Daily Show where he served as a correspondent from 2005 to 2007. After leaving The Daily Show in 2007, he has since moved to Los Angeles with his family and filmed supporting roles in the films Observe and Report and Horrible Bosses. He also appeared in the Snake 'N Bacon animated special on Adult Swim, which aired on May 10, 2009. In early 2010, he co-starred in the comedy pilot "Our Show" on NBC.
Through late 2010 and early 2011, Bakkedahl began appearing in a series of commercials for T-Mobile cellular phones, where he plays a human likeness of AT&T's 3G network.
Bakkedahl guest starred as a waiter in an episode of HBO's Curb Your Enthusiasm titled "The Hero" which debuted on August 14, 2011.
Bakkedahl is a member of the advisory council of the California Shakespeare Theater.