The College Initiative was founded in 2002 by its current director, Benay Rubenstein, a prison educator with a 20-year history of developing and coordinating in-prison college programs. In 1994, after the loss of federal Pell and New York State TAP grants for prisoners (the primary funding sources for higher education programs in prisons until that time), Benay re-directed her attention to meeting the needs of released prisoners who wanted to attend college, but lacked the practical knowledge and support to do so.
During its first four years, CI was housed by Episcopal Social Services under the leadership of Executive Director, Stephen Chinlund, former chairman of the New York State Commission of Corrections. In May 2006, CI joined the City University of New York (CUNY). This move gave CI direct access to the vast resources of the largest public university system in the nation.
In July 2007, CI became an Incubator Project of the Fund for the City of New York moving from John Jay College of Criminal Justice to a permanent home base on CUNY's Lehman Campus. This move enabled CI to work closely with its sizable cohort of Lehman students who are enrolled in the Bachelor of Arts in Social Work or Adult Degree Program through the Division of Adult and Continuing Education. CI is a member of the CUNY-wide Black Male Initiative, directed by Elliott Dawes.
In 2008, CI opened a satellite office at The Fortune Society's headquarters in Long Island City, Queens. CI's bi-weekly orientation sessions for new students and free College Prep program are based at the Fortune facility.