 Thompson was a two-year starter at Penn State, he passed for six touchdowns as a junior in 1998 and led the Nittany Lions to a win over Kentucky in the Outback Bowl, in which he threw for 187 yards and a touchdown.As a senior, Thompson was a team captain and threw 13 touchdown passes and averaged 159.7 passing yards-per-game.He did not play in the Nittany Lions' 24-0 shutout of Texas A&M in the 1999 Alamo Bowl due to a shoulder injury sustained earlier in the week.