The UCSD "Energy Center" commenced operation informally during the fall of 1972 under the impetus of Professor Sanford S. Penner. Formally designated as an organized research unit on July 1, 1974, the Energy Center addressed applications that varied in response to university needs. This center was given a new name, the Center for Energy and Combustion Research (CECR) in 1986 to underscore the close link between energy and combustion research. Prof. Forman A. Williams, whose research specialty is combustion, succeeded S. S. Penner as director in 1990.

On July 1, 2000, the Center combined with the Fusion Energy Research Program and the Virtual Laboratory for Technology at UCSD, and again changed its name, to the present name, the Center for Energy Research (CER). The combination of these different energy-related activities on campus into a single center formed the basis for expanding the scope of the center.

On July 1, 2006, Farrokh Najmabadi, Professor of Electrical and Computer Engineering, became the 3rd director of the Center. As recommended in the 15-year review of the Center, he is committed to broadening the Center's research agenda to include new initiatives in areas such as bio-fuels and solar energy that will build on the Center's strengths in combustion and fusion research and will help to address California's and the nation's critical energy-related challenges.