Thomas Nee joined the UC San Diego Music Department in 1967, soon becoming artistic director and conductor of the La Jolla Symphony and Chorus. He chaired the department of music at UCSD from 1971 to 1974. He retired from UCSD in 1991.

When he retired from the La Jolla Symphony in 1998, the Thomas Nee Commission was established to commission annual new works from graduates of UC San Diego's music composition program.

A longtime Encinitas resident, Nee died July 7, 2008, of complications from kidney disease. He was 87.

In 2013, his paternal grandson Alex Nee played the lead role of Johnny in the Green Day musical American Idiot.