The first issue of The Prairie Naturalist appeared in March 1968. The North Dakota Natural Science Society published this quarterly peer-reviewed journal as a means of communicating research on the natural history and environment of North Dakota and the Great Plains region. Issues included full-length articles with detailed scientific research, in addition to short notes and book reviews. Dr. Paul B. Kannowski of the Institute for Ecological Studies at the University of North Dakota was editor of the journal from its beginning until 2004.

The North Dakota Natural Science Society changed its name to the Great Plains Natural Science Society in 2004, due to the large number of members residing outside of North Dakota. As of 2008, The Prairie Naturalist is published at Fort Hays State University in Fort Hays, Kansas. The journal is abstracted in several professional abstract journals, including Biological Abstracts, Fisheries Review and Wildlife Review.