CEE evolved from a regional organization, the Western Regional Environmental Education Council (WREEC), which began through a series of informal meetings and communications initiated by Rudolph J. H. Schafer, then Environmental Education Coordinator for the California Department of Education, and Dave Phillips of the US Office of Education. A grant of $150,000 was obtained through US Office of Education (Title V, Section 505) to fund a three-year project. The original funding allowed the 13 western states to begin developing environmental education programs, to set up formal and informal working relationships between the education and resource management agencies, and to enhance cooperation among their respective groups. In 1973, WREEC formally established itself as an incorporated, non-profit 501(c)(3) educational organization to prolong the momentum and mission of these newly organizing states.

Due to perseverance on the part of the original founders, many meetings and mini-conferences (of the resource agencies and education departments) were held throughout the west from 1970 until 1976. The gatherings were intended: to assist participating state education and resource management agencies in examining the status of environmental education, and to identify roles, relationships and responsibilities for the program; and to assist state education and resource management agencies to improve the effectiveness of their environmental education programs through intrastate cooperation.  As the various agencies and education department meetings grew and expanded, so did the list of participants. For example, the National Park Service, the US Environmental Protection Agency, US Job Corps and others began to recognize the value of this growing effort. The commitment and activities of WREEC in the early years resulted in major accomplishments for environmental education nationally.

WREEC's first pioneering program, developed with the American Forest Institute (now American Forest Foundation) was Project Learning Tree--an award-winning interdisciplinary environmental education program that focuses on forests to introduce youth to conservation and ecological concepts.  WREEC's second major program, Project WILD, was developed in partnership with the Western Association of Fish and Wildlife Agencies (WAFWA). In 1991, WREEC entered into a partnership with The Watercourse (formerly Western Watercourse) to develop Project WET (Water Education for Teachers) as its third national initiative in environmental education and became the official co-sponsor for the program.

Through the years, as support for WREEC's co-sponsored programs expanded beyond the western states, WREEC's network for environmental education continued to grow. In 1996, WREEC officially changed its name to the Council for Environmental Education (CEE) to more accurately reflect the national reach of its co-sponsored programs.  The purposes of the Council remain as they have been over the years: to support environmental education through the management and development of environmental education programs, to publish and disseminate environmental education materials, and to facilitate the development and maintenance of partnerships for environmental education.

For 34 years, the CEE has been a nationally recognized leader in environmental education, providing programs and services that promote responsible stewardship of natural resources. CEE administers Project WILD, Project WILD Aquatic, WET in the City, Team WET Schools, and Flying WILD at the national level.