Pier A was built from 1884 to 1886 to serve the New York City Department of Docks and Harbor Police. The engineer in charge of construction and design was George Sears Greene Jr, the son of the civil engineer and Union general George S. Greene.
The design mirrored the Statue of Liberty which could be viewed from a similar but shorter tower. The roof was tin, painted green to resemble copper. In renovation by the Battery Park City Authority this roof was discarded, and replaced with copper.
The pier was expanded in 1900 and again in 1919 with a clock installed in the pier's tower as a memorial to 116,000 US servicemen who died during World War I. The clock is a ship's clock and was donated by Daniel G. Reid, founder of United States Steel Corporation.
The clock was unveiled at noon on January 25, 1919 by Rear Admiral Josiah S. McKean, with speeches made by Mayor John Francis Hylan and Docks Commissioner George Murray Hulbert. It is said to be the first World War I memorial erected in the United States.
The New York City Fire Department used the pier from 1960 to 1992 as a fireboat station. In 1991, the American Merchant Mariners' Memorial was installed on a rebuilt stone breakwater just south of Pier A, connected to it by a dock. Designed by the sculptor Marisol Escobar, the memorial depicts four merchant seamen with their sinking vessel after it had been attacked by a U-boat during World War II. One of the seamen is in the water, and is covered by the sea with each high tide.
From 1992 onward, the pier was vacant and fell into disrepair. Several proposals for redevelopment fell through.
A restoration of the pier commenced in 2009. Pier A's restaurant and bar, "Pier A Harbor House", opened to the public in November 2014.