Thompson was part of the Hundred Days Men enlistment program near the end of the American Civil War.

[4][9] In the 1870 census,[10] Thompson was listed as living in Normal, Illinois, with his wife Ellen, mother Mary, as well as Emma and John Powell.

In 1867, Thompson's brother-in-law, John Wesley Powell, organized an expedition to the Rocky Mountains to collect specimens for the Illinois State Natural History Society.

They secured supplies at Fort Bridger and Salt Lake City to be shipped to three locations along the expedition route.

Along with other members of the survey, he left Kanab, Utah, on May 30, 1872, to identify a passage to the mouth of the Dirty Devil River, where the Second Expedition crew had stored a boat.

[12] Ellen Powell Thompson accompanied her husband on some of his surveying activities, including trips into the mountains and boating the rapids of southern Utah.

Ultimately, Thompson constructed maps of Utah, Wyoming, Arizona, and Nevada based on field work from the Powell expeditions.

The April 25, 1878 Winfield (KS) Courier reported that Thompson was exploring locations to start a sheep business in Kansas.

[15] In the early 1880s, Thompson began work for the U.S. Geological Survey under the new USGS director, John Wesley Powell.

[18] Thompson also devised a survey instrument used during geographical operations to provide measurements that could be used in determining the irrigable land.

[19] Thompson was part of a tight-knit community of explorers, scientists and businessmen in Washington, D.C., interested in forming a geographic society.

[23] In a report submitted July 1, 1893, Thompson described work conducted in all of the western states and the establishment of new field offices in California, Idaho, Oregon, and Washington.

He stated that "a geographic name should be short, euphonic, pronounced as spelled, and have a meaning or express some sentiment to help fix it in the memory".

[28] In choosing geographic names during the Powell expeditions, Thompson selected a combination of Piute terms such as Kaibab and Toroweap, Mormon pioneer terms like Pipe Springs and Wild Band Pockets, and also used descriptive words like Tantalus Creek and Thousand Lakes Mountain.

[4] Frederick Dellenbaugh, author of The Romance of the Colorado River and a fellow member of the Second Expedition, stated that "to his (Thompson's) foresight, rare good judgment, ability to think out a plan to the last minute detail, fine nerve and absolute lack of any kind of foolishness, together with a wide knowledge and intelligence, this expedition, and indeed the scientific work so admirably carried on by the United States Survey of the Rocky Mountain region and the Geological Survey for three decades in the Far West, largely own success".