With the conviction that healthcare is the right of all and must be provided regardless of socioeconomic or health status, three New York University (NYU) medical students established the NYU Free Clinic Project in the fall of 1999.

One year later, the Institute for Family Health (IFH) partnered with NYU School of Medicine (NYU SOM) and the NYU Free Clinic Project to form the New York City Free Clinic (NYCFC).

The Association of American Medical Colleges (AAMC) and Pfizer awarded the NYCFC the Caring for the Community start-up grant in late 2000. With the management infrastructure in place by the spring of 2001, the NYCFC opened to the public on March 9, 2002.

One month later, IFH received substantial funding from the Starr Foundation. Funding was awarded to support operational and administrative costs associated with IFH's partnership with the NYCFC. The Starr Foundation continued its strong financial support of the NYCFC until 2009.

The NYCFC is currently funded through the Robin Hood Foundation and private donations.