ISERP is descended from the Bureau for Applied Social Research (BASR), established in 1944 by sociologist Paul F. Lazarsfeld after the Rockefeller Princeton Radio Project moved to Columbia University. The Bureau secured Columbia’s place as a pioneering institution in the social sciences, making landmark contributions to mass communications research, public opinion polling, organizational studies, and social science methodology. After Lazarsfeld's death in 1976, the legacy of the bureau was carried on by the Center for the Social Sciences, which was later renamed in Lazarsfeld's honor. Under directors Harold Watts, Jonathan Cole, and Harrison White, the Center continued the tradition of pushing the boundaries of social scientific methodology and interdisciplinary research, particularly in the areas of sociology of science and network analysis.

The Paul F. Lazarsfeld Center for the Social Sciences was incorporated into what was then called the Institute for Social and Economic Theory and Research (ISETR) at its founding in 1999. Joining the Center at ISETR were the Center for Urban Research and Policy, founded in 1992, and a number of new research centers. In 2001, ISETR merged with the Office of Sponsored Research at Columbia’s School of International and Public Affairs, and changed its name to reflect the broadened scope of its activities.