The Nonprofit Center of Northeast Florida traces its roots to a 1998 study of the community's nonprofit sector conducted by Jacksonville Community Council Inc. (JCCI). The study identified the "lack of an organizational vehicle" as one of the sector's major shortcomings and recommended establishment of "an organization to support and advocate for a strengthened nonprofit sector in Northeast Florida."
A group of community leaders and advocates for the nonprofit sector spent the subsequent four years building support for the Nonprofit Center of Northeast Florida and establishing its corporate structure.
In summer 2002, after conducting a national search, the Nonprofit Center opened its doors with Jonathan Lever as Executive Director and with its operating budget funded for its first three years.
On October 29, 2002, the Nonprofit Center held its official launch at the Ritz Theater. Several hundred nonprofit executives and community leaders attended.