Santa Clara has won 11 Conference Pennants, and appeared in 12 NCAA Tournaments, including a runner-up finish in the 1962 College World Series.

Early managers like Billy Hulen, Joe Corbett, Jay Hughes, Jimmy Byrnes, and Patsy O'Rourke were all former major league players who had made the trek west to coach baseball at what was the known as Santa Clara College.

Another Bronco baseball player from the early period was Harry Wolter, who recorded the first hit in then-new Fenway Park as a member of the Red Sox.

Graham then embarked on a baseball career which saw him rise from obscurity in the western minor leagues to becoming the starting catcher for the Boston Americans, and star pitcher Cy Young.

He returned home, and ultimately became the owner of the San Francisco Seals, and donated generously to Santa Clara and the baseball program.

However, the competitiveness of the Santa Clara teams from prior to 1946 is exhibited in the number of Major League players produced in this period, notably Harry Wolter (Major League debut in 1907), Elmer Stricklett (1904), Hardin Barry (1912), Justin Fitzgerald (1911), Hal Chase (1905), Charlie Graham (1906), Tillie Shafer (1908), Frank Arellanes (1908), William Hogan (1911), Erv Kantlehner (1914), Frank Shellenback (1918), Bevo LeBourveau (1919), Bill Lawrence (1932), Jim O'Connell (1923), Marv Owen (1931), and Les Powers (1938).

Following the end of the war, Santa Clara returned to the diamond and found immediate success under John "Paddy" Cottrell, who coached the team from 1946 to 1951.

Though Santa Clara stumbled in Cottrell's first year at the helm, in 1962 the Broncos jumped out to an impressive start, and held the #1 spot in the polls for almost the entirety of the 1962 season.

The baseball crazed Bay Area, who had just received their first major league franchises a few years earlier, lent their full support to the Broncos.

Led by five future major leaguers – Bob Garibaldi, Ernie Fazio, John Boccabella, Pete Magrini, and Tim Cullen, the Broncos found their way to the College World Series finals.

The Broncos reeled off Conference championships and NCAA tournament appearances for four consecutive years, followed by three straight second-place finishes, setting the early tone that Santa Clara would be a name to respect in WCC baseball.

While at the helm of the Broncos, Mark O'Brien and his staff were said to have struggled to compete in recruiting while playing at the outdated multi-purpose Buck Shaw Stadium.

Santa Clara responded by building the $8.6 million Stephen Schott Stadium, a 1,500 seat state-of-the-art baseball specific venue that is one of the finest facilities of its size on the West Coast.

The stadium was financed in large part by Santa Clara Alumnus Stephen Schott, a varsity baseball player in 1960, and at that time, owner of the Oakland Athletics.

Mark O'Brien's tenure was not without notable products—Santa Clara's Daniel Nava made an improbable run from SCU baseball manager to a contributing player on the 2013 Red Sox, who won the world series, and Santa Clara's Tommy Medica made his MLB debut in 2013 for the San Diego Padres.

Following the loss of the top five pitchers from 2012, Santa Clara sank to its lowest baseball nadir, finishing in last for the second year in a row with a 1–23 mark in the WCC.

O'Brien vowed to return to Santa Clara to the baseball prominence it had enjoyed for nearly 110 years prior to the struggles of the Broncos since the retirement of John Oldham.

Rusty Filter was brought in as the 44th manager of the Santa Clara Baseball program in June 2017; after spending the previous eight years at Stanford where he was among the top pitching coaches in the nation.

The 1,500-seat stadium houses the entire Santa Clara baseball program, including its training, practice and equipment facilities.