Kowalsky started teaching clarinet at the Eastman School of Music in Interlochen in the mid-seventies and worked at the Eastman School of Music from 1975 to 1984. He joined the faculty at the Florida State University in 1984 and became a principal clarinet of the Tallahassee Symphony Orchestra the same year. In 1990, Frank was appointed a full professor at FSU. Kowalsky served as a Joseph A. White Professor of Music from 2001 until his retirement in 2013.

As a guest performer, Frank Kowalsky had been appearing with Naples Philharmonic Orchestra, Seattle Symphony Orchestra, Rochester Philharmonic Orchestra, Northwood Orchestra, the Colorado Philharmonic, and other prominent American ensembles.