Pirner was born in Green Bay, Wisconsin. By the time he was seventeen, Pirner was living and working in Minneapolis, Minnesota. He taught himself how to play the drums. By age 20, Pirner started his career drumming with a punk band called Loud Fast Rules as part of the Minneapolis scene, together with Karl Mueller (bass) and Dan Murphy (guitar). When Pirner switched to singing and playing rhythm guitar, Pat Morley joined on drums. Morley was later replaced by Grant Young, and the band changed their name to Soul Asylum. After touring the United States for a number of years they gathered a cult following of fans, but did not quite reach commercial visibility. Pirner at the time was the band's songwriter and he produced the album, Coup De Grace, by the Minneapolis metal band the Coup de Grace in 1990.
In November 2013 it was announced that Pirner would be appearing as a guest vocalist on the upcoming Within Temptation album, "Hydra", on the track 'Whole World Is Watching'.