PRI was founded in 1932 by Gilbert D. Harris (1864-1952), a professor of geology at Cornell University from 1895 to 1934. A man of varied talents and interests, Harris had started his own scientific journal, Bulletins of American Paleontology, which he printed on his own press, in 1895. During his long career he also trained many well-known paleontologists and was a noted petroleum geologist and a world authority on Cenozoic paleontology. Unconvinced that Cornell would care for his legacy after his retirement, Harris obtained a charter for his own independent scientific enterprise from New York State.

On June 28, 1932, in a small ceremony attended by friends and students, Harris laid the cornerstone for the first PRI building, on a piece of property next to his house in the Cornell Heights section of Ithaca. He continued to pursue his research, add to the collections, and print his journals for another two decades.

Harris’ student and protégée Katherine V.W. Palmer (1895-1982) became PRI's second Director in 1952. Herself a widely respected paleontologist, Palmer moved PRI to larger quarters (its present site) on Ithaca’s West Hill in 1968, where she continued the publications, cared for the collections, and set up the Institution’s first small public museum space. She retired in 1978, at the age of 83.

The 1980s were a time of stasis at PRI. Publications were the focus of most activity; research, exhibit, and education programs were neglected; collections and physical plant were allowed to deteriorate. In 1991, however, PRI's Board of Trustees recommitted the Institution to its entire four-fold mission of research, publication, collections care, and public education, and Warren D. Allmon was hired as PRI's fourth Director in 1992.

Allmon restarted research and public educational outreach, raised funds from the National Science Foundation for collections care, and established connections with Cornell, including teaching of undergraduate and graduate students. The staff and specimen collections expanded significantly. In 1998 a 6,000 square foot collections and exhibits addition was completed.

In 2003, PRI opened the Museum of the Earth, an $11 million natural history museum. In 2004, PRI and Cornell signed a formal affiliation agreement, ending 70 years of official estrangement.

In 2008, a half-time endowed professorship was established for the PRI Director in Cornell’s Department of Earth and Atmospheric Sciences.

In 2013 PRI took over the nearby Cayuga Nature Center and Smith Woods, broadening its educational outreach to include all natural history of the Finger Lakes region.

PRI is today a national leader in Earth science education, especially around climate change, and provides educational content and teacher professional development resources across the country. More than 900,000 people visited PRI’s online resources in 2021.

The PRI collection of more than seven million specimens is one of the ten largest in the nation. Bulletins of American Paleontology recently published its 400th issue, and is one of the oldest paleontological journals in the world.

PRI's staff of about 30 includes seven PhDs, and the annual operating budget is around $3 million.

The new banners hanging in the parking lot at the Museum of the Earth signify the 20th anniversary of the Museum, 10th anniversary of the merger with Cayuga Nature Center, and the 90th anniversary of PRI.

2022 marks PRI's 90th anniversary and just in the last 30 years, PRI has made major significant impacts in the local Ithaca community by establishing the Museum of the Earth and merging with Cayuga Nature Center.