He spent most of the fifties and sixties in Minneapolis, working as a music director of the Civic Orchestra of Minneapolis and Minnesota Opera. Thomas also was an assistant conductor of the Minneapolis Symphony Orchestra under Antal Dorati.

In 1967, Nee joined the faculty of UCSD and became an artistic director and conductor of La Jolla Symphony, remaining in that role for over 30 years. Together with Will Ogdon and Robert Erickson, who were also students of innovative composer Ernst Krenek, Thomas Nee developed a program in the spirit of their teacher's "learning by making music" approach. He chaired the University Of California, San Diego from 1971 to 1974 and conducted The SONOR Ensemble Of UCSD.

During his tenure at UC San Diego, many prominent composers held residences at the University guiding and mentoring students, including John Cage, Toru Takemitsu, and Iannis Xenakis. Thomas Nee retired from the University in 1991.