Thomas attended Scotch Plains-Fanwood High School in Scotch Plains, New Jersey during his freshman and sophomore years. For his junior and senior years, he attended Saint Benedict's Preparatory School. He led the school to two Prep A Division New Jersey State titles with a 56–3 record in his final two seasons while averaging 14.5 points and 6.5 rebounds per game his senior year. In 2005, Thomas played at the USA Basketball Youth Development Festival where he helped the Blue Team win the silver medal with a 3–1 record. Following his senior year, he played in the 2006 McDonald's All-American game.

Considered a four-star recruit by Rivals.com, Thomas was listed as the No. 13 small forward and the No. 42 player in the nation in 2006.

After committing to Duke University on April 5, 2006, Thomas played for the Under 18 national team at the FIBA Americas Under-18 Championship where he helped USA win the gold medal.

Sources:

As a freshman, Thomas averaged 4.0 points and 2.5 rebounds per game, while shooting .568 from the field, in 31 games (18 starts).

""Best game offensively I've played in a Duke uniform. I feel like I've played better games for this team, not including having 21 points. I mean, my game is not defined by how many points I have. But if I can bring a mix of both, and it would be great.""

As a sophomore, Thomas averaged 4.3 points and 3.3 rebounds in 18.5 minutes in 32 games (28 starts). He posted a .505 field goal percentage and recorded at least five rebounds 12 times, including eight of Duke's 16 ACC games.

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