After graduating from the Naval Academy in June 1859, he served with the Africa Squadron until September 1861 when he sailed a prize slaver home to the United States. Lieutenant Farquhar spent most of the Civil War off the U.S. Atlantic coast and in the West Indies, serving in the gunboats, and, and the cruiser. At the close of the war, he was executive officer of the gunboat. He was promoted to the rank of Lieutenant Commander in August 1865, a few months after the fighting ended, and was on duty at the U.S. Naval Academy from then until September 1868. For the rest of the 1860s and into the next decade, Farquhar served in the screw sloop, was Executive Officer of the sloop and the frigate, and Commanding Officer of the gunboat. He also had two tours at the Boston Navy Yard on ordnance duty and as Executive Officer. Advanced in rank to Commander in December 1872, Farquhar spent nearly five years at the Naval Academy. He commanded the training ship in 1877-78, and the steam sloops and in European waters in 1878-1881. Five more years of Naval Academy duty were followed by torpedo instruction at Newport, Rhode Island, in 1886. From May 1887 until her loss in the March 1889 Samoan hurricane, Captain Farquhar commanded the steam frigate. Farquhar was commended for his fine handling of his ship during that disastrous 1889 hurricane at Apia, Samoa, in which she and a number of other American and foreign naval vessels were lost. He then served on several of the Navy's boards and, in March 1890 became the Chief of the Bureau of Yards and Docks. During 1894-97, he was Commandant of the Philadelphia Navy Yard, Commanding Officer of the cruiser, and President of the Naval Examining Board. While holding the ranks of Commodore and Rear Admiral, Farquhar was Commandant of the Norfolk Navy Yard in 1897-99, commanded the North Atlantic Squadron during 1899-1901 and was Chairman of the Lighthouse Board in 1901-02. Admiral Farquhar was a companion of the Military Order of the Loyal Legion of the United States and a member of the Naval Order of the United States. Rear Admiral Farquhar retired on 11 April 1902, and died at Jamestown, Rhode Island on 3 July 1907. Farquhar was buried in Section 1 of Arlington National Cemetery. His wife, Addie Whelan Pope Farquhar, is buried with him.
