The Lewis & Clark Interpretive Center Fund, Inc. was created in 1991 by several of Montana's leading citizens in partnership with the US Forest Service, the federal agency entrusted with management of the Center. This non-profit organization was incorporated to provide the resources and leadership necessary to generate funds needed to build the original facility in the 1990s. By 1995, Fund, Inc. had successfully raised $3 million to match a federal appropriation of an additional $3 million, which funded construction of the Lewis and Clark National Historic Trail Interpretive Center.

On October 1, 2010 the Lewis & Clark Interpretive Center Foundation merged with the Lewis and Clark Interpretive Association, and began operating under a new name: the Lewis & Clark Foundation. The Portage Cache Store became a part of Foundation operations.