Jordan studied biology at Cornell University (M.S., 1872) and became professor of biology at Butler University, Indianapolis, Ind., before being appointed professor of natural history at Indiana University, Bloomington, in 1879. He became president of that university in 1885. In 1891 he became the first president of the newly opened Leland Stanford Junior University (now Stanford University), in Stanford, Calif., and he served in this post until 1913.

Jordan was inspired to specialize in ichthyology by the Swiss-born American naturalist Louis Agassiz. From the 1870s, Jordan made extensive field trips in the United States and its coastal areas, and his efforts led to the naming of a total of 1,085 genera and more than 2,500 species of fishes (fish), together with broader classifications of them. With B.W. Evermann he wrote the authoritative “The Fishes of North and Middle America,” and his Manual of the Vertebrates of the Northern United States went through 13 editions between its publication in 1876 and 1929. Jordan devoted his later career mainly to the cause of international peace, acting as chief director of the World Peace Foundation.