NINLHE was founded in 1993 and established as a s a 501(c)(3) corporation by Dr. Colleen Larimore and Dr. Jim Larimore, the former directors of the Native American programs at Dartmouth College and Stanford University. With funding from the Intel Foundation, NINLHE began as a strategic, self-help coalition of a dozen directors from the most successful Native student retention programs in the country. Though the directors faced nearly identical challenges on respective home campuses, at that time, each worked in isolation from one another. They realized that by working together they could do much to help themselves, and by extension, all of the students. By coming together through an organization as NINLHE, it offered the opportunity to expand the impact to effect much needed change in Native education practice and policy at the institutional and national levels as well.
NINLHE's success as a national professional higher education organization since its inception has been achieved through the support of several philanthropic organizations. These include: