The school's team currently competes in the Atlantic 10 Conference and plays its home games at the Reilly Center.

In 1916, Butler Gym was constructed, but wasn't finished by the time the intercollegiate team played its first game against University at Buffalo.

Following World War II, Anslem Kreiger, a former All-American Basketball player, took over the program, with a record of 15-10 over his two-year tenure.

[3][4] Ed (Melvin) Milkovich took over the basketball team for a six-year period starting with the 1948–49 season, after Kreiger was promoted to athletic director.

This was a period of great success for the program, with two appearances in the National Invitational Tournament (NIT), the first during the 1950–51 season when the team was eliminated in the second round.

In 1970, St. Bonaventure, led by future NBA-great Bob Lanier, was thought to have a legitimate shot at unseating UCLA for the national title.

In each Final Four game, the Lanier-less Bonnies were dominated by the opponent's pivot, Artis Gilmore for Jacksonville and Sam Lacey for New Mexico State.

In the 1999–2000 season, the Bonnies finished in second place in A-10 play under coach Jim Baron and lost to #6 ranked Temple in the A-10 tournament championship.

The 2002–03 men's basketball season was marred by a scandal after a transfer student from a junior college, Jamil Terrell, was permitted to play even though he had not completed his associate degree and was therefore ineligible for one year.

Head coach Jan van Breda Kolff, athletic director Gothard Lane, and school president Dr. Robert Wickenheiser were all ousted.

[8] St. Bonaventure's chairman of the board of trustees, William Swan, took his own life in August 2003, feeling that he had let down his alma mater by failing to prevent the scandal.

[9] St. Bonaventure docked itself three scholarships from 2003 to 2005 and the NCAA subsequently put the team on three years' probation and banned it from postseason play in 2003–04.

Led by conference Player of the Year Andrew Nicholson — the 19th pick by Orlando in the 2012 NBA draft — they accumulated a 20–12 record during the regular season.

The conference title earned them an automatic bid to the NCAA tournament, where they lost 66–63 to ACC champion Florida State in the second round at Bridgestone Arena in Nashville, Tennessee.

On February 7, 2015, Bonnies guard Marcus Posley hit a buzzer beater shot to upset the nationally ranked VCU Rams and Shaka Smart at the nearly sold-out Reilly Center.

[14][15] Their omission was widely considered to be one of the largest snubs of the year, if not all time, being the first team to ever to have an RPI ranking in the top 30 and a conference regular season title to their name, and not receive a bid.

It came as such a surprise to so many in the college basketball world, that it prompted the Atlantic 10 athletic director to issue a public statement voicing her dissatisfaction with the committee's decision to exclude the Bonnies.

[14] The following year, St. Bonaventure alum Brian Toolan wrote a short book about the Bonnies' 2015-2016 season, entitled "Snubbed".

[19] On February 27, 2021 the Bonnies clinched the first ever outright Atlantic 10 regular season title in program history when Davidson defeated VCU 65-57.

They defeated Colorado, Oklahoma and Virginia en route to an appearance at Madison Square Garden for the NIT semifinals versus Xavier.

Following the loss, the "ironman 5 2.0" as they were called composed of Kyle Lofton, Dominick Welch, Jaren Holmes, Jalen Adaway and Osun Osunniyi all opted to take their talents elsewhere.

† The Associated Press began compiling a ranking of the top 20 college men's basketball teams during the 1948–1949 season.

In July 2023, the university announced that it was unable to come to an agreement with the station's current owners to continue broadcasting the games.

I think our station and Bonaventure were competing directly against each other for the advertising dollars that we needed to cover our costs and turn a profit.