John Wilson Shaffer (July 5, 1827 – October 31, 1870) was an American politician and businessman who served as the 7th Governor of Utah Territory.

Born in Lewisburg, Pennsylvania, Shaffer was active in Republican politics in Illinois.

He was elected clerk and recorder for the Illinois Circuit Court for Stephenson County.

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.