John Wilson Shaffer (July 5, 1827 – October 31, 1870) was an American political leader. Born in Lewisburg, Pennsylvania, Shaffer was active in Republican poliitics in Illinois and served in the Union Army during the American Civil War. He was appointed governor of the territory of Utah by President Ulysses S. Grant. He was known for his strict opposition of any hint of rebellion against the federal government, which led to concerns with the Mormon population. He died suddenly during his first year as governor.