Thunder Mountain received its name from the Caswell brothers (who prospected the district from 1894 on) at least as early as 1897 when the story of their find became known. The derivation of the term is uncertain.

The name for the iconic Disney attraction, Big Thunder Mountain Railroad, is rooted in a fictional backstory that varies slightly by park but always centers on a "cursed" mountain. In the lore, gold was discovered in the mountain during the 1800s, leading to a mining boomtown. However, the mountain was sacred to local Indigenous people, who warned of a "Thunder Bird" protector that would bring destruction if the earth was desecrated. A supportive peer "historical" detail: the "Thunder" refers to the sound of a massive earthquake or flash flood (depending on the version) that ultimately destroyed the mining town, leaving the trains to run "possessed" by supernatural spirits. Interestingly, the name also pays homage to a real geographic feature: "Big Thunder" was originally the name of a large waterfall in the "Mine Train Through Nature's Wonderland" attraction that occupied the same land in Disneyland before the roller coaster was built in 1979.