The NCAA Division I program has been a member of the West Coast Conference since 1996 and its home venue is Washington Trust Field and Patterson Baseball Complex, opened on Gonzaga's campus in 2007.

Gonzaga College was founded in September 1887, and the first recorded game of the baseball program was held shortly thereafter, in 1890.

[2][3] On September 14, 1910, Dave Skeels became the first Gonzaga player to appear in the major leagues when he pitched in a game for the Detroit Tigers.

[13][14] Larry Koentopp was named head coach prior to the 1970 season, and the Big Sky expanded to eight teams that summer.

The Zags won the Big Sky championship series in three of those four seasons,[12] which earned a berth in the NCAA tournament in 1971,[17][18] 1973,[19][20] and 1974.

[28][29] Along with Idaho and Boise State, the program joined the new seven-team Northern Pacific Conference (NorPac) in June 1974.

The team used Spokane's Avista Stadium until its current venue, Washington Trust Field and Patterson Baseball Complex, was completed prior to the 2007 season.

After losing to San Diego in 2007, Gonzaga defeated Loyola Marymount in 2009 to qualify for the program's first NCAA tournament since 1981.

[10] In 2016, as a sophomore future major leaguer Eli Morgan was 10–3 with a 3.73 ERA in 16 starts,[57] earning him a spot on the All-West Coast Conference (WCC) First Team.

[65] The team moved from Underhill to its first on-campus home, located in Gonzaga's upper campus, where it played until after the 1966 season.

[71] For three seasons (2004–2006), Gonzaga played at Avista Stadium, the home venue of the minor league Spokane Indians.

[72] At the start of the 2007 season, the program opened its current venue, Washington Trust Field and Patterson Baseball Complex.

[54][73] It was dedicated a month later on April 20, named for Washington Trust Bank, a donor to the field's construction, and Michael Patterson, a Gonzaga alumnus.

[74] Steve Hertz is the winningest and longest-tenured head coach in Gonzaga athletics history; in 24 seasons (1978, 1981–2003) at the helm, he recorded 637 wins.

[88][89] Pitcher Eli Morgan was selected by the Cleveland Indians in the eighth round of the 2017 Major League Baseball draft.