Founder Sean Forman began developing the website while working on his Ph.D. dissertation in applied math and computational science at the University of Iowa.

It was originally built as a web interface to the Lahman Baseball Database, though it now employs a variety of data sources.

[3] In 2006, Forman left his job as a math professor at Saint Joseph's University in order to focus on Baseball Reference full-time.

[5] At the end of April 2021, the site changed a number of identifying names, "discontinuing the use of nicknames that are racially or ethnically influenced" and "names based upon a player's disability", such as Chief Bender and Dummy Hoy, who are now listed as Charles Bender and Billy Hoy, respectively.

It also offers sabermetrician Jay Jaffe's system acronymmed "JAWS" method for ranking players of different eras against each other by weighting their primes.