Big Thunder Mountain Railroad was designed by Imagineer Tony Baxter and ride design engineer Bill Watkins. The concept came from Baxter's work on fellow Imagineer Marc Davis's concept for the Western River Expedition, a western-themed pavilion at the Magic Kingdom, designed to look like an enormous plateau and contain many rides, including a runaway mine train roller coaster. However, because the pavilion as a whole was deemed too expensive in light of the 1973 construction and opening of Pirates of the Caribbean, Baxter proposed severing the mine train and building it as a separate attraction.

The Big Thunder Mountain Railroad project was put on hold again in 1974 as resources and personnel were being diverted to work on constructing Space Mountain in Tomorrowland, but this delay may have ultimately produced a smoother ride as the use of computers in attraction design was just beginning when the project was resumed. Big Thunder Mountain Railroad was one of the first Disney rides to utilize computer-aided design. The attraction first opened at Disneyland in 1979, and the Magic Kingdom's larger version in Florida opened in 1980. Tokyo Disneyland's version opened in 1987 and Disneyland Paris opened with its version in 1992. The Paris version's layout and structure were mostly based on the Florida version of the ride, but with several significant differences.

The revised European ride takes the form of a large island in the center of the Rivers of the Far West, accessed from its riverside station by tunnels underneath the water. The attraction in Disneyland Paris is the only Big Thunder Mountain to have been an opening-day attraction at its park. Hong Kong Disneyland does not have a Big Thunder Mountain Railroad attraction (or a western-themed Frontierland, for that matter). However, Grizzly Gulch has a theme similar to Frontierland. The main attraction, Big Grizzly Mountain Runaway Mine Cars, carries a similar theme to Big Thunder Mountain Railroad.

For the most part, the track layout of the Magic Kingdom's version is a mirror image of the Disneyland version.

Riders board the trains in an enclosed loading station on a hillside. Leaving the station, trains make a left hand turn into a bat-infested tunnel, make a slight right turn, and climb the first lift hill. At the top of the lift hill, trains pass under a waterfall and drop to the left. This is followed by a right hand turn, after which the track crosses under the second lift hill and drop. After crossing under the second lift hill drop, the track goes through a 270 degree clockwise spiral and passes through a short tunnel. Trains emerge from the tunnel and pass through the flooded town of Tumbleweed. The train passes over a decaying trestle (where the track is slightly banked from side to side), before entering Davy Jones Mine, where it hits a trim brake. Trains then make a left hand turn and climb the second lift hill.

At the top of the second lift hill, trains drop to the left and cross under the lift hill, before rising into a 540 degree downhill counterclockwise helix, passing over a broken trestle. Leaving the helix, trains shoot up across a small hill, make a slight right turn, then drop through another tunnel and hit a trim brake. The trains then make a right hand turn into a tunnel and climb the third lift hill. As the train climbs the lift, an earthquake hits and makes the train cars sway from side to side (the effect achieved by slightly banking the track). Leaving the lift, trains emerge from the tunnel, crest a small rise, and drop to the left towards the Rivers of America. After traveling along a short section of straight track, the ride then makes a left hand turn through a short tunnel and crosses a short bridge. The train then makes a right hand turn, and passes through the ribcage of a T-Rex skeleton as it hits the final trim brake, makes a left hand turn past some geysers and hot springs, and rises into the final brakes. The train then coasts back to the station.

The Florida version was allocated more space in the park, and so the Monument Valley-inspired ride structure assumes 2.5 acres, 25 percent larger than the Disneyland version.