Malkmus studied at the University of Virginia history. After graduating he founded with Scott Kannenberg 1989 Pavement and David Berman, the group The Silver Jews. In 1996, he was seen on the side of Janeane Garofalo in the film Sweethearts. Published in 1997 Malkmus with members of the band Silkworm under the name The Crust Brothers, the live cover album Marquee Mark, on the including five Bob Dylan songs can be heard.
After the separation of Pavement Malkmus played from 1999 with Kim Gordon, Ikue Mori, Thurston Moore and Jim O'Rourke short time under the name of Kim 's Bedroom together, however, the group released no recordings.
In 2000, Malkmus recorded his first solo album. He was assisted by the Decemberists drummer John Moen and bassist Joanna Bolme, who then played in the band Stephen Malkmus and the Jicks. It was followed by two more albums, each of which received mostly positive reviews in media such as Pitchfork Media. Both albums made it into the Billboard charts, the Pig Lib number 97 who reached the top 100. On 7 March 2008 appeared Malkmus ' album Real Emotional Trash, on the place John Moen, the drummer Janet Weiss Sleater - Kinney is heard.
Malkmus married in 2006, has two daughters and lives in Portland (Oregon ). Since August 2011, Malkmus and his family lived for a time in Berlin. and led the album Ege Bamyasi Can Sebastian flower ( synthesizer), Felix Hedderichstraße (bass ), Jan Philipp Janzen (drums) and Phillip Tielsch (guitar) from the band Von Spar on.