Thompson was named to three All-America teams following the 2012-13 season. He became the first NABC All-American in program history with second team honors, while also earning a spot on the DIII News fifth team and D3hoops.com honorable mention.
Thompson reached a number of milestones in his senior season. He became just the seventh Statesman to record 1,500 career points. Thompson amassed a total of 1,643 career points which put him fourth on Hobart's all-time scoring list. He also became the only Statesman to score more than 1,000 points and record more than 400 assists. Thompson ranks second on the Hobart list with 492 career assists. He was also the first member of the Hobart basketball team to play in the NABC/Reese's Division III College All Star Game, where he posted 12 points, four rebounds and three assists.
The three-time All-Liberty League selection and 2012-13 Liberty League Player of the Year finished this season atop the conference with 5.4 assists per game and a 2.3 assist-to-turnover. Thompson ranked fourth in scoring (15.6 ppg), free throw percentage (.841) and minutes played (34.6), fifth in 3-point field goal percentage (.422) and sixth in 3-points field goals made (1.9).
Thompson earned All-East honors from the NABC and D3hoops.com in his junior and senior seasons. As a first-year, Thompson was named the Rookie of the Year for the Liberty League as well as the D3hoops.com East Region and the ECAC Upstate Region.