In 1985, the CDIPD was founded as an NIH-NIAID-supported Tropical Disease Research Unit (TDRU) at University of California, 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 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.