The Roger Tory Peterson Institute of Natural History can trace its roots to 1975 when M. Lorimer Moe, a longtime friend of Peterson's, formed a committee along with John D. Hamilton (President of the Gebbie Foundation of Jamestown, New York) and several other community members to plan an organization to honor Jamestown's most famous son.  In 1984 the Institute was granted 501(c)(3) tax-exempt status by the I.R.S. and received a Provisional Charter as an educational institution from the University of the State New York.

The Institute's first executive director was hired in 1984, its first director of education in 1989.  By 1993 (the year the Robert A. M. Stern-designed headquarters building was completed) the Institute had a reputation for quality nature education programs, wildlife art and nature photography exhibits, and national forums with published proceedings on nature education related topics. The primary source of funding from 1984 to 1993 was the Gebbie Foundation of Jamestown and the State of New York.

The years 1994 and 1995 found the Institute without the start-up funding from its two largest donors and with a growing program and a new 26,000-square-foot building to support.  This very stressful time was followed by extreme cost cutting and the growth of a donor base that, eventually, put the Institute on a paying basis.

On July 28, 1996, Roger Tory Peterson died at the age of 87.  Since then, the Institute has accessioned a very large amount of Peterson's body of work and has become the key destination for those interested in Peterson's contributions to science and society as the great naturalist of the 20th century.

In 2000 the Roger Tory Peterson Institute of Natural History Foundation was founded with the sole purpose of managing the permanently restricted endowment funds and supporting operations of the Institute with its income.
 
In 2004 the Institute filed a breach of contract lawsuit against unrelated family members of Peterson's third wife who took possession of items contracted to, but not yet received by, the Institute.  The lawsuit was settled in August 2006, and the Institute received the final items of original art and photography resulting from the settlement in June 2008.

In recent years the Institute has partnered with colleges and universities to offer courses for teachers and developed programs for the Internet to more effectively reach its nationwide audience. For example, the Institute's Electronic Naturalist website has become a premier online resource for teachers that has won several awards.

In August 2008 the Institute began a year-long celebration of the Centennial of Roger Tory Peterson's birth. Highlights of the Centennial Celebration include a major exhibition of Peterson's life work, a nature writer speaker's series, and a national birding festival to be held in June 2009.