Parker attended Bartram Trail High School in St. Johns County, Florida. He played both baseball and football and was a highly regarded recruit in both sports. He came out of high school as the #34 overall player in the country and #4 quarterback in the country according to ESPN. While he was the #13 quarterback by Scout. Parker first started at quarterback the last five games of his sophomore season where he threw for 870 yards and rushed for 450. In his junior year he threw for 1,850 yards and rushed for 700 while accounting for 27 touchdowns. He was also invited to the Under Armour All-American game, where he threw the game winning touchdown pass. In baseball he was a first team all state and county selection his junior season. He did not play his senior season due to him enrolling at Clemson in January 2008 of his senior year.
After spending 2008 as a redshirt freshman, Parker started all 14 of the Tigers games at quarterback. He finished the season completing 205 of 369 passes for 2,526 yards with 20 touchdowns and 12 interceptions. The pass completions, passing yards and touchdowns were all Clemson freshman records. He was named a second-team freshman All-American by College Football News and a first-team freshman All-ACC by Sporting News. He guided Clemson to nine wins his freshman year with those numbers. One of those wins was against a top ten team on the road in Miami where he threw three touchdowns. He led the Tigers to 34 points in seven different games. Against N.C. State, Wake Forest and, Middle Tennessee State he was named the team's offensive player of the week. In the game against Miami he threw for 326 yards which is the second best ever for a Clemson quarterback and also threw four touchdowns in a game which is tied for the record. Also had a streak with at least one touchdown pass in seven straight games. He ended up throwing for over 200 yards in five games and had over 200 yards of total offense in seven. He ended the season in seventh in both passing yards and ratings at 180.4 and 124.4 respectively. In Clemson's bowl game he threw for 141 yards and a touchdown in a bowl win over Kentucky. He was the first freshman quarterback to take his team to a conference championship game. He was also the first Clemson freshman to start in a bowl win.
As a freshman in 2008, Parker was a first-team freshman All-American by Baseball America after he hit .303 with 14 home runs and 50 runs batted in in 57 games.He was also a first-team All-ACC selection his freshman year. He led his team in home runs and was second in slugging percentage at .559 and, walks at thirty two. In ACC play he batted .336 with ten home runs, thirty four RBIs and a .441 on-base percentage in 29 ACC games. He was tied for second in home runs, was second in RBIs, and fifth in slugging percentage. He had a streak in May where he had an RBI in nine straight games. Parker was named ACC player of the week on April 28. He had five games in that stretch where he batted .375 while scoring six runs, having two doubles, three home runs and twelve RBIs. As a junior in 2009, Parker hit .255 with 12 home runs and 52 RBIs in 63 games. He started sixty games. Forty nine were in right field and eleven as the designated hitter. In ACC play Parker hit .295 with seven home runs and 23 RBIs in 27 games. He also hit a team-high seven times. In the Clemson and South Carolina series he was given the Bob Bradley Award for being Clemson's MVP. He batted .400 with a home run, seven RBIs, four runs, and a walk. He was named ACC player of the week again on April 13 for batting .444 with two home runs, eleven RBIs, four runs, and three walks. During the season he had a streak of seven straight hits - one shy of the school record. Parker also had an amazing day on April 11 where he went 3-for-7 with two home runs, five RBIs, and three runs in a doubleheader. Earlier that day he played quarterback for the Tigers in the spring football game where he threw 171 yards and a touchdown. Parker was also chosen to the All-ACC preseason team and was ranked as the #32 player in the country. He is also the first Division I athlete ever to throw twenty touchdown passes and hit twenty home runs in the same academic year.