Halligan, born on 4 May 1876 in South Boston, Massachusetts, graduated from the United States Naval Academy at the head of his class in 1898.

He served during the Spanish–American War in the armored cruiser USS Brooklyn, flagship of Commodore Winfield S. Schley.

Naval Forces, France, and for his outstanding performance of duty he received the Distinguished Service Medal.

After the Armistice, he commanded the battleship Ohio, and in 1925 became chief of the Bureau of Engineering with the temporary rank of rear admiral.

Appointed Rear Admiral in 1930, Halligan died at Puget Sound, Washington, 11 December 1934, while serving as Commandant, 13th Naval District.