Koerner grew up in Rochester, New York, and after a brief military service attended the University of Minnesota. He intended to major in engineering but soon became involved in the Minneapolis music scene, where he met Dave Ray and Tony Glover. They formed a loose-knit trio, releasing albums under the name Koerner, Ray & Glover. The group gained notice with their first album, Blues, Rags and Hollers, originally released by Audiophile in 1963 and re-released by Elektra Records later that year.

In 1965, Koerner recorded his first solo album, Spider Blues, for Elektra and appeared at the Newport Folk Festival accompanied by Glover. He continued playing on the folk circuit and joined with Willie Murphy to record Running, Jumping, Standing Still in 1969. The duo eventually split up, and Koerner pursued an unsuccessful career in filmmaking, retiring from music and moving to Copenhagen, Denmark. He later returned to music in the traditional folk genre and continued to perform and release new albums from time to time. He now lives in Minneapolis and has two sons and a daughter.

In 1983 the Minnesota Music Academy named Koerner, Ray and Glover “Best Folk Group” and in 1985 inducted them into the MMA Hall of Fame.

In 2008, Koerner, Ray & Glover were inducted into the Minnesota Blues Hall of Fame under the category Blues Recordings for Blues, Rags and Hollers.