The Beckman Center opened its doors May 1989 with a $12 million gift from the Arnold and Mabel Beckman Foundation, which covered one-fifth of the nearly $60 million construction and outfitting costs. The project, completed on time and under budget, was completely funded by private sources.

The founding of the Center represented an unprecedented expansion of the basic sciences at Stanford. With its establishment, the School of Medicine was able to house 20 new faculty members and create two new academic departments, Molecular and Cellular Physiology and Developmental Biology. Joining these were the Howard Hughes Medical Institute (HHMI) Unit and the well known Department of Biochemistry, with its two Nobel laureates and seven National Academy of Sciences members.

In its 26 years of operation, the Beckman Center has become a powerhouse of basic research within the School of Medicine. The first decade focused on building bridges between basic and clinical research activities at the Stanford School of Medicine. In 1999, the Beckman Fellows program was established to support young investigators. In 2002, Beckman became pivotal to Dean Philip Pizzo's large-scale strategic plan to emphasize interaction among all university departments, becoming the inspiration for Bio-X, a program designed specifically to bring together leading-edge research in basic, applied, and clinical sciences.