The CDIPD has its origins in 1985 as an NIH-NIAID-supported Tropical Disease Research Unit (TDRU) at UC San Francisco under the directorship of Professor James H. McKerrow. The TDRU focused on drug development for Chagas disease targeting a specific parasite-derived proteolytic enzyme. The interdisciplinary science that now characterizes the CDIPD grew from this initial effort. Members of the TDRU included parasitologists, chemists, computational scientists, structural biologists and biochemists. In 2002, Herb and Marion Sandler made a groundbreaking gift to UC San Francisco to expand the TDRU into the Sandler Center for Basic Research in Parasitic Diseases. The basic and applied research expanded into several other parasitic diseases of global health importance, including schistosomiasis, filariasis, Human African Trypanosomiasis and amebiasis. In 2009, the Center was named the Sandler Center for Drug Discovery with a stronger focus on the discovery and development of drugs for neglected parasitic diseases, and including additional parasitic diseases, such as hookworm, giardiasis and primary amebic meningoencephalitis.   

In 2012, the Center for Discovery and Innovation in Parasitic Diseases (CDIPD) was instituted to continue the interdisciplinary research effort for diseases associated with poverty, combined with a stronger educational emphasis on advocacy, outreach, training and capacity-building which characterize the goals of the center today. In 2014, the CDIPD relocated to the Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, when Jim McKerrow became Dean of the school. Upon his retirement as the school’s Dean in 2022, Conor Caffrey became Director of the CDIPD.