Joseph K. Barnes (July 21, 1817 – April 5, 1883) was an American physician and the 12th Surgeon General of the United States Army (1864–1882).

He later studied medicine with Surgeon General Thomas Harris of the United States Navy, and received his medical degree from the University of Pennsylvania in 1838.

Barnes appeared before an army examining board which was meeting at the time in Philadelphia and, pursuant to its recommendation, he was commissioned an assistant surgeon on June 15, 1840.

After only a few months of duty, he was ordered to accompany a detachment of recruits to Florida, where hostilities were in progress against the Seminole Indians.

Notable in his field service of this period was his accompanying Brigadier General Willam Harney's expedition through the Everglades during the Second Seminole War.

During the advance upon Mexico City, he was chief surgeon of the cavalry brigade and participated in the battles of Cerro Gordo, Contreras, Churubusco, and Molina del Rey, in the storming of Chapultepec and the capture of the capital.

During the thirteen years that intervened between this time and the Civil War, Barnes served in a succession of posts in widely separated parts of the country.

In April 1861, Barnes was stationed at the Army's Fort Vancouver in Washington Territory, the second-ranking officer behind future Union general Edward Ord.

While on this duty he formed the acquaintance of U.S. Secretary of War Edwin M. Stanton, who quickly gained a highly favorable impression of him.

It was but a few weeks after this advancement that the difficulties between Stanton and Surgeon General William Alexander Hammond culminated in the detachment of the latter from his office.

A War Department order of April 7, 1862, placed them under the supervision of the Surgeon General, but was not sufficiently explicit in its provisions regarding the right of command of the medical officers in charge of these hospitals.