Thompson was the brother of fellow raider Dauphin Adolphus Thompson. During the raid, he was captured outside the engine house on October 17 while carrying a white flag of truce and held prisoner in a hotel. After the killing of Harpers Ferry Mayor Fontaine Beckham, Thompson's captors became enraged, took him to the railroad bridge, and killed him. Then, they tossed his body off the bridge and used his body for target practice all day.