After originally signing a letter of intent to play college football with Notre Dame in 1995, Moss took part in a racially-charged fight at his high school that left one person hospitalized. He entered a plea of guilty to battery, and received probation along with a 30-day suspended jail sentence. Notre Dame subsequently revoked his scholarship, but this did not stop another high-profile college football program from giving him a chance. Notre Dame officials suggested he attend Florida State due to the reputation of its coach, Bobby Bowden, for handling troubled players. However, because of his signed letter of intent at Notre Dame, the NCAA considered him a transfer student, which made him ineligible to play for the Seminoles in the 1995 football season. He was red-shirted in his freshman season. While at Florida State, Moss ran a 4.25 40-yard dash while only Deion Sanders, with a 4.23 40-yard dash, had achieved better.
In 1996, while serving his 30-day jail sentence in a work-release program from 1995, Moss tested positive for smoking marijuana, thus violating his probation, and was let go by Florida State. He served an additional 60 days in jail for the probation violation.
Ultimately, Moss transferred to Marshall University, about an hour's drive from his home. Because Marshall was then a Division I-AA school, NCAA rules allowed him to transfer there without losing any further eligibility. In 1996, he set the NCAA Division I-AA records for most games with a touchdown catch in a season (14), most consecutive games with a touchdown catch (13), most touchdown passes caught by a freshman in a season (29), and most receiving yards gained by a freshman in a season (1709 on 78 catches), record which still stands. Moss was also the leading kickoff returner in Division I-AA on the season, with 484 total yards and a 34.6 yard average. Marshall went undefeated and won the Division I-AA title in its last season before moving to Division I-A.