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The first intercollegiate baseball game took place in Pittsfield, Massachusetts, on July 1, 1859, between squads representing Amherst College and Williams College. Amherst won, 73–32. This game was one of the last played under an earlier version of the game known as "Massachusetts rules", which prevailed in New England until the "Knickerbocker Rules" (or "New York Rules") developed in the 1840s gradually became accepted. The first ever nine-man team college baseball game under the Knickerbocker Rules still in use today was played in New York on November 3, 1859, between the Fordham Rose Hill Baseball Club of St. John's College (now Fordham University) against The College of St. Francis Xavier, now known as Xavier High School.

Students at many colleges began organizing games between colleges, particularly after the Civil War, first in the northeastern United States but quickly throughout the country. By the late 1870s, several northeastern schools were playing regular home and home series. The team with the best record claimed a "National Championship." Arguments over professional and graduate players led to the creation of the American College Base Ball Association in late 1879, consisting of six northeastern schools which sought to govern such issues and organize games. This organization lasted until 1887, when it dissolved in acrimony and waves of realignment. The Western Conference and Southern Intercollegiate Athletic Association were formed in the 1890s as multi-sport conferences. The first tournament to name a national champion was held at the 1893 World's Fair in Chicago, resulting in Yale being crowned champion. No other such tournament was held until the first College World Series in 1947.

Traditionally, college baseball has been played in the early part of the year, with a relatively short schedule and during a time when cold (and/or rainy) weather hinders the ability for games to be played, particularly in the northern and midwestern parts of the U.S. These and other factors have historically led colleges and universities across the nation to effectively consider baseball a minor sport, both in scholarships as well as money and other points of emphasis.

College baseball's popularity has increased greatly since the 1980s.^[] As increased efforts to popularize the sport resulted in better players and overall programs, more television and print media coverage began to emerge. The ESPN family of networks have greatly increased television coverage of the NCAA playoffs and the College World Series since 2003.^[]

For 2008 and succeeding seasons, the NCAA mandated the first ever start date for Division I baseball, thirteen weeks before the selection of the NCAA tournament field, which takes place on Memorial Day.^[]