Joseph Sylvester O'Halloran was born on March 28, 1842, in Adelaide, Australia, the son of Captain William Littlejohn O'Halloran (1806-1885) and Eliza Minton Smith (1810-1884).

He was a civil servant. He was educated at private schools and entered the South Australian Civil Service, receiving his first appointment at Governor Sir Richard Graves MacDonnell's office. After passing ten years in the Audit Office, he was promoted to the clerkship of the Executive Council. He also served as a gazetted Clerk to the Court of Appeals and a private secretary to the Right Hon. Sir James Fergusson, 6th Baronet, Governor of the colony. O'Halloran retired from the Government service in 1871 and moved to England, where he was elected a Fellow of the Royal Geographical Society and the Royal Colonial Institute. He travelled to New Zealand (1873) and the Cape of Good Hope (1877). In 1881, he was appointed assistant secretary and librarian of the Royal Colonial Institute, and in 1883, to the position of its secretary until 1909. He visited Canada in 1882 and 1884, attending the Montreal meeting of the British Association for the Advancement of Science as one of the secretaries to the Geographical Section. Before returning to England, he made an extended tour through Nova Scotia, New Brunswick, and Prince Edward Island. O'Halloran was a contributor to the Dictionary of National Biography (as J. S. O'H).

In 1886, he married Alice Mary Simpson (1853–1923). He died on January 25, 1920, in Cheltenham, Gloucestershire, England.