[4][5] The town began life in the late nineteenth century as a station stop on the Denver and Rio Grande Western Railroad (D&RGW), which had been completed through the area in 1883.

)[6] The town was a community center for the small number of farmers and ranchers living in the inhospitable region, and it was also a prominent shipping point for cattle that were run in the Book Cliffs area.

Thompson gained importance in the early twentieth century due to the development of coal mines in Sego Canyon, north of town.

For many years the city was served by various D&RGW passenger trains, including the Scenic Limited, the Exposition Flyer, the Prospector, the California Zephyr (where it was a flag stop, though the timetable for 1969 shows it as a regular stop), and the Rio Grande Zephyr.

Subsequently, for the next fourteen years, the city was served by various Amtrak trains, including the California Zephyr, the Desert Wind, and the Pioneer.

Construction of I-70 two miles south of Thompson Springs drew traffic away from the city as the former Old Cisco Highway (US 6 and US-50)[7] (now named Frontage Road) was no longer used.

The Union Pacific Railroad runs through Thompson Springs, but Amtrak service via a flag stop was discontinued in 1994.

The district includes several well-preserved groups petroglyphs (images etched into the rock surface) and pictographs (images painted onto the rock surface) left by early Native Americans in three different styles (each with their own panel): Fremont, Ute and Barrier Canyon.