Thiemens moved to the department of chemistry at the University of California San Diego in 1980, where he was hired as an assistant professor as a replacement for Hans Seuss and took over the laboratory of Nobel Laureate Harold Urey. He was promoted to full professor in 1989, and served as the chair of the department of chemistry and biochemistry from 1996-1999. He was the founding dean of the division of physical sciences and served from 1999-2016.