Andy Stokes caught 32 passes for 417 yards (13.0 avg.) and a pair of touchdowns as a sophomore. The following year, he caught 30 passes for 408 yards (13.6 avg.) and three scores, adding 23 yards on three rushing attempts (7.7 avg.) and also posted five tackles (4 solos) on special teams. For that performance, he was named All-Mid-States Football Association honorable mention.
In 2004, Stokes was awarded third-team NAIA All-America and first-team All-MSFA honors. He was also named to Football Gazette's all-region team. He finished second on the team with a career-high 42 receptions for 753 yards (17.9 avg.) and five touchdowns. He ran once for 16 yards, threw an option pass for 39 yards and recorded four tackles. In 31 games with the Statesmen, Stokes snatched 104 passes for 1,578 yards (15.2 avg.) and 10 touchdowns. He rushed four times for 39 yards (9.8 avg.) and had a 39-yard pass completion. He also recorded nine tackles (6 solos).