Chowning was born in Salem, New Jersey in 1934. Following military service and four years at Wittenberg University in Ohio (B. of Mus), he studied composition from1959-61 in Paris with Nadia Boulanger.  He received the doctorate in composition (DMA) from Stanford University in 1966, where he studied with Leland Smith.  In 1964 setup the he set up a computer music program using the computer system of Stanford's Artificial Intelligence Laboratory. Beginning the same year he began the research that led to the first generalized surround sound localization algorithm in the digital domain.  In trying to comprehend the distance cue, Chowning discovered frequency modulation synthesis (FM) in 1967. This breakthrough in the synthesis of timbres allowed a very simple yet elegant way of creating and controlling time-varying spectra.

He taught computer-sound synthesis and composition at Stanford University's Department of Music beginning in 1966.  In 1974, with John Grey, James (Andy) Moorer, Loren Rush and Leland Smith, he founded the Center for Computer Research in Music and Acoustics (CCRMA), which remains one of the leading centers for computer music and related research. Although he retired in 1996, he has remained involved in activities at CCRMA. In 2019 he initiated a long term project to recreate, by means of computer modeling, the acoustics of the Chauvet Cave in France as they were when the exquisite 32,000-year-old wall paintings were created.