The College of Idaho has a rich history of intercollegiate athletics dating back over a century, with success on and off the court and field. Coyote men's teams include soccer, cross country, and football in the fall; basketball, swimming, and indoor track in the winter; and baseball, golf, lacrosse, and outdoor track in the spring. The Coyote women compete in soccer, cross country, and volleyball in the fall; basketball, swimming, and indoor track in the winter; and softball, golf, tennis, and outdoor track in the spring.

The Coyote basketball, baseball, and cross country programs have been among the best in the Northwest over the past three decades. The basketball team has advanced to 27 NAIA National Championship events, winning the 2023 and 2025 NAIA National Championships and the 1996 NAIA Division II National title, as well as advancing to the national semifinals in 2018 and 2019. The baseball team advanced to the postseason every year from 1987-2012, winning the 1998 NAIA National Championship. The team also sent star pitcher Riley O'Brien to the MLB in 2017, where he was an eighth-round draft pick. The women's cross country team has won the last six Cascade Conference titles, including the 2023 NAIA National Championship. The men's cross country team has won the conference title four of the last six years and won the 2024 NAIA National Championship. 

Over the past two decades, The C of I has fielded one of the more successful women's intercollegiate athletic programs in the Pacific Northwest. Six sports - basketball, volleyball, cross country, swim, softball, and track & field - have finished in the Top-10 of their respective national tournaments, and each of the 9 women's teams has had success on the field, court, and track. The C of I volleyball team won eight-straight Cascade Conference titles from 2006-13 and advanced to 11 NAIA National Championships. The cross country program has made 17-straight trips to the NAIA Championships- placing second in 2012, 2013, and 2019, winning CCC titles in 2008, 2009, 2011, 2012, 2013, 2019, and 2023, and the 2023 NAIA National Championship. The basketball team advanced to five-straight NAIA Division II National Championships from 2009-13, and the softball team made trips to the NAIA National Championships in 2008, 2009, 2013, 2014, 2019, 2021, 2022, and 2024. Both the swim and track & field teams send countless competitors to their respective national events, with Hillary Holt becoming C of I's first women's track National Champion in 2012 (finishing her career with 11 NAIA titles). The swim team placed fifth at the 2020 NAIA Championships and was named the 2024-25 Fall Scholar All-America Team by the CSCAA. The soccer program advanced to the postseason each year from 2006-11 and every season since 2015. The golf program ranked in the NAIA Top-25 each year from 2011-13, earning their first-ever berth to Nationals. The tennis team was also among the best NAIA programs in the Northwest during the 1990s.

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