[1] The American Civil War broke out in April 1861, and Higginson's first assignment after graduation was to the screw frigate USS Colorado, which was operating under the command of Captain Theodorus Bailey in the West Gulf Blockading Squadron off the United States Gulf Coast as part of the Union blockade of the Confederate States of America.

While aboard Colorado, Higginson was wounded on September 14, 1861, while participating in a raid against Pensacola, Florida, in which a party from Colorado captured and destroyed the schooner Judah or Judith,[note 2] which was believed to be undergoing conversion for service as a Confederate privateer, and spiked a gun of a Confederate artillery battery at the Pensacola Navy Yard.

[1][2] Detaching from Colorado in 1862, Higginson became signal midshipman and aide to Bailey aboard the gunboat USS Cayuga, and was aboard Cayuga serving in that capacity as Bailey commanded a gunboat division during the Battle of Forts Jackson and St. Philip on the Mississippi River in Louisiana on April 24, 1862.

He was executive officer of the gunboat USS Marblehead when she participated in the search for the Confederate States Navy commerce raider CSS Tallahassee in August 1864.

Naval Academy in 1865, and later that year reported aboard the sloop-of-war USS Hartford, the flagship of the East India Squadron, as a watch officer.

Naval Academy again in September 1873, but in November 1873 reported back aboard Franklin in the European Squadron for a tour as her executive officer, just in time for orders to arrive for the European, North Atlantic, and South Atlantic squadrons to concentrate at Key West, Florida, in case the Virginius Affair that arose that month resulted in a war with Spain.

It took until early February 1874 for all units of the three squadrons to arrive at Key West, by which time the crisis had passed, but the three squadrons did engage that month in the first open-ocean tactical exercises by a multi-ship force in the history of the U.S. Navy, whose training and operations – other than those in coastal waters and rivers during the Civil War – previously had been limited to single ships operating individually.

After she steamed from Philadelphia, Pennsylvania, to New York City for completion, he detached from her and on August 23, 1883, took command of the gunboat USS Monocacy in the Asiatic Squadron; under his command, Monocacy, protected American interests during the Battle of Foo Chow of August 23–26, 1884, in which the French Navy's Far East Squadron under Admiral Amédée Courbet bombarded the arsenal at Foo Chow, China, and virtually destroyed the Chinese Navy's Fujian Fleet.

He was captain of the yard there from June 1896 to July 1897, when he became commanding officer of the battleship USS Massachusetts in the North Atlantic Squadron.

[7] During the blockade, Massachusetts was among ships exchanging fire with Spanish coastal fortifications and the armored cruiser Cristóbal Colón on May 31, 1898.

Massachusetts remained involved in the blockade but missed the climactic Battle of Santiago de Cuba on July 3, 1898, because she was away coaling at Guantánamo Bay.

[5] In September 1902, he commanded the squadron during a war game in which 16 of its ships simulated an attack on U.S. Army coastal fortifications along the U.S. East Coast.