HealthCare Choices (HCC) was founded in 2001 by the Institute for Community Living (ICL), another not-for-profit organization. A trusted provider of mental health and developmental disabilities services throughout Brooklyn, the Bronx, Manhattan, and Queens, ICL started HCC because it was serving thousands of individuals with developmental and psychiatric disabilities who were having trouble accessing quality health care, yet were at serious risk due to serious but controllable chronic health disorders.

HCC's first site was 6209 16th Avenue in Brooklyn, where it still offers comprehensive medical, dental and mental health care in one location. An NYS-licensed Article 28 diagnostic and treatment center, HCC more recently in 2010 received NCQA certification as a Level 3 Patient-centered Medical Home.

In recent years because of HCC's expertise with special-needs populations and the high quality of its health service, organizations that operate NYC Department of Homeless Services (DHS)-funded homeless facilities (including ICL) have contracted with HCC to provide on-site health care. Homeless individuals travel to one of the HCC locations for specialty medical and/or dental care.

In 2009, HCC received an NYS HEAL grant and matching funding from the NYS Department of Homeless Services to support development of a new Article 28 health clinic in Long Island City Queens, adjacent to the Borden Avenue Veterans Residence (BAVR). BAVR is a NYC Department of Homeless Services transitional facility for homeless veterans. HCC’s Queens clinic opened its doors in the fall of 2011, providing male and female veterans of all wars, people who are homeless, people with special needs and the community at large with integrated medical, dental and mental health care services.

In 2011, the federal Health Resources and Services Administration (HRSA) awarded HCC Federally Qualified Health Center (FQHC) designation and an operating grant for its Brooklyn and Queens clinics, one of 10 awards to new applications nationally that year. The grant is supporting HCC's expansion from serving 1,200 adults to 4,200 people of all ages between the two clinics, with a special focus on New Yorkers who are homeless and/or have special needs.

In 2011, HCC established itself as an independent organization with a Board reflective of the communities it serves and the people who receive health care from HCC.