William Lewis Stoughton (March 20, 1827 – June 6, 1888) was a politician and soldier from U.S. state of Michigan who served in the United States Congress, as well as serving as an officer and brigade commander in the Union Army during the American Civil War.

Stoughton was a prosecuting attorney of St. Joseph County from 1855 to 1859 and a delegate to the 1860 Republican National Convention.

Stoughton commanded the 2nd Brigade, 1st Division of the XIV Corps of the Army of the Cumberland at the Battle of Chattanooga.

He resigned in August 1864 because of ill health and resumed the practice of his profession in Sturgis, Michigan, in 1865.

On February 28, 1867, President Andrew Johnson nominated Stoughton for appointment to the grade of brevet major general of volunteers, to rank from March 13, 1865, and the United States Senate confirmed the appointment on March 2, 1867.