Born in 1956 in New York City, Krakauer started out on piano before switching to clarinet at age nine. He took classical lessons and he eventually discovered the music of jazz clarinetist Sydney Bechet. After high school, he studied music, ultimately completing his master's degree at Juilliard -- where he studied under Leon Russianoff. He also studied at Sarah Lawrence College and the Paris Conservatory. While in his early twenties, Krakauer shifted away from jazz to focus on his classical career. However, in the '80s, Krakauer began playing klezmer, in part as a way to further embrace his Eastern European Jewish cultural heritage. This renewed his passion for improvisation, and soon he was composing his own brand of modern klezmer that combined traditional forms with jazz, funk, and avant-garde influences, as well as allowing him to explore the sonic possibilities of the clarinet. In 1988, he joined the boundary-pushing ensemble the Klezmatics, appearing on their first three albums: Shvaygn = Toyt, Rhythm + Jews, and Jews with Horns.
Krakauer went on to lead the equally genre-bending Klezmer Madness, debuting the group on their 1995 eponymously titled Klezmer Madness! for John Zorn's Tzadik label. Concurrent to Zorn's Radical Jewish Culture movement, Krakauer helped to launch the klezmer revival from the early '90s onward. The following year, he joined with the Kronos Quartet, exploring yet more Judaic themes on Osvaldo Golijov: The Dream and Prayers of Isaac the Blind. The album received the Diapason d'Or in France.
In the 2000s, he recorded a series of albums for Label Bleu, beginning with 2001's A New Hot One. He then returned to his work with Klezmer Madness for 2002's The Twelve Tribes which took home album of the year in Germany's Preis der Deutschen Schallplattenkritik. Another Klezmer Madness effort, Bubbemeises: Lies My Gramma Told Me, arrived in 2005. That same year, he played on composer Paul Moravec's Pulitzer Prize-winning Tempest Fantasy. He has also recorded with violinist Itzhak Perlman, vocalist Dawn Upshaw, Continuum, Randy Sandke, and others. In 2012, Krakauer released Masada Book 2: The Book of Angels, Vol. 18: Pruflas, which found him playing songs from John Zorn's Masada project.
In 2014, he released Dreams Prayers, which received a Grammy nomination for Krakauer as a soloist with the conductorless chamber orchestra for the piece "A Far Cry." At the same time, he debuted his Ancestral Groove band on Checkpoint. He can also be heard on notable recordings by David Del Tredici, the Albany Symphony Orchestra, Stefan Weglowski, as well as on the scores to films by Danny Elfman, Sally Potter, Ang Lee, and Eric Steel. As a performer, Krakauer has appeared with a bevy of artists and ensembles, including the WDR Big Band, John Cage, the Philadelphia Orchestra, Fred Wesley, the Emerson Quartet, Marin Alsop, Leonard Slatkin, and Anakronic Electro Orkestra, among others. Krakauer has also garnered attention as a composer, co-composing several large works with pianist/composer Kathleen Tagg. In 2022, he and Tagg debuted their adventurous Mazel Tov Cocktail Party! project. ~ Matt Collar, Rovi