Parker was appointed a midshipman March 11, 1837. He was attached to the West Indian Squadron, then transferred to the Philadelphia Naval School, graduating in 1843. In 1842, he served under his father, Foxhall A. Parker Sr., in Constitution. He also served under his father in Brandywine. On September 21, 1850, he was commissioned lieutenant. He served against the Florida Indians, on the Great Lakes, the Mediterranean, the Pacific, and on various coast surveys.[1]
From 1861 to 1862, he was executive officer of the navy yard at Washington, D.C. During the Civil War, he cooperated with the Army of the Potomac, protecting Alexandria, Virginia, after the First Battle of Bull Run. His capable manipulation of the forces at his command went far toward restoring order and confidence at Washington. He built Fort Dahlgren, and drilled 2,000 seamen in the exercise of artillery and small arms, thereby promoting the success of Admiral Andrew H. Foote's operations with the Mississippi Flotilla.
He became commander on July 16, 1862, had charge of the steam gunboat Mahaska in active service off Wilmington and Yorktown, and of the gunboat Wabash off Charleston from June to September 1863. He commanded a naval battery at the bombardment of Fort Sumter. Later, until the close of the war, he commanded the Potomac Flotilla, which consisted at one time of 42 vessels, and frequently engaged Confederate forces.