The cross country program was reinstated in 2000 after a brief existence in the 1980s. The team won the Illinois Skyway Collegiate Conference championship in 2016 and 2004 and the NJCAA Region IV championship in 2017 and 2004. As a team, they have appeared in the NJCAA national tournament four times (2017, 2008, 2005 and 2004), but several individual runners have competed at nationals every year since 2001.

In 2017 and 2016, the Cyclones earned Academic All-NJCAA Team designation from the National Junior College Cross Country Coaches Association, finishing with the second highest GPA in the country both years among Division I colleges.

Former runners Wes Sewell and Kevin Deegan were named Individual Champion-Most Valuable Runner in 2007 and 2004, respectively. Jordi Rangel earned the honor in 2016. Deegan (2005, 2004) transferred to Western Illinois University, where he tied for the top all-time indoor performance in the 1,000-meter run (2:27.71) and took second in the 800-meter run (1:50.66).

Eight runners have been named to the All-NJCAA Region IV and All-Illinois Skyway Collegiate Conference teams both years they competed at Moraine Valley: David Alvarez (2018, 2017), Diego Arana (2018, 2017), Rangel (2017, 2016), Jeremy Morgan (2016, 2015), Dawid Palac (2014, 2013), Eric Schmidt (2005, 2004), Deegan (2005, 2004) and Matt Swiatkowski (2003, 2002).

Since the program was reinstated in 2000, 27 men have been named NJCAA Cross Country Scholar All-Americans.