Having completed his training both at sea and in the classroom, Upshur was graduated from the United States Naval Academy on 10 August 1848 as a passed midshipman.

[1] Unlike cousin Robert E. Lee, Upshur stayed with the Union military during the American Civil War, resisting much family pressure to choose the Confederacy.

Promoted to lieutenant commander, 16 July 1862, Upshur served in the South Atlantic Blockading Squadron in charge of the steamer USS Flambeau from 1862 to 1863[1] during operations against Charleston.

He returned to the North Atlantic Blockading Squadron in time for the abortive joint expedition against Fort Fisher late in December 1864.

[1] After the Civil War, Upshur served in a succession of sea and shore billets, promoted to commander, 25 July 1866, and given the USS Frolic, on the Mediterranean station, in 1865–1867.

[5] He commissioned the building in 1884, with design by architect Frederick C. Withers, a Queen Anne home, later known as United States Daughters of 1812, National Headquarters.