The university sponsors thirteen teams including men and women's basketball, cross country, tennis, and track and field; women's-only golf, soccer, softball, and volleyball; and men's-only football.

In October 2009 Idaho State University Director of Athletics Jeff Tingey announced that the contract of head football coach John Zamberlin would be extended for two more years, meaning Zamberin was on the Bengals sidelines manning the program through the 2011 season.

The administration have stood by their decision, citing an increase in athlete attendance in classes and graduation rates as a direct result of Zamberlin's coaching.

Zamberlin was fired and former Eastern Washington and Montana State coach, Mike Kramer, was hired.

In March 1977, the men's basketball team made national headlines by defeating the UCLA Bruins 76–75 in the West regional semifinal of that year's NCAA tournament.

[6] The most recent appearance of the women's team in the NCAA tournament was in 2021, when it was eliminated 71–63 in the first round by the Kentucky Wildcats.

[7] The women's program maintained an active rivalry in basketball with both Idaho and Boise State.

[15][16][17] The Bengals won the southern division in their final season,[18] and met north champion Gonzaga in the best-of-three championship series in Pocatello.

[14][21][22][23] Boise State and Idaho dropped their baseball programs six years later in 1980, citing budget constraints.

[24][25] Idaho State won 8 Big Sky titles (1967, 1968, 1969, 1970, 1971, 1972, 1973, 1984) in wrestling, starting with its first in 1967;[26][27] the sport was dropped by the conference 38 years ago, after the 1987 season.