The present Fort Gilkicker replaced an earlier one constructed in 1856 on the same site, this was known as Monckton Auxiliary Battery. The Royal Commission of 1860 recommended that the first battery should be extended and strengthened, instead a new fort was built and its name changed to Fort Gilkicker.
It was intended as a coast defence battery to cover the beach at Stokes Bay, already defended by a line of ditch and rampart with five flanking batteries, known as the Stokes Bay Lines, and the deep water anchorage off Browndown as well as the inner approaches to Portsmouth Harbour. It was proposed as ‘a battery of curved form for 26 guns on one tier’. It was to direct its principal fire on Stourbridge Shoal and the flanks on Spithead and Stokes Bay. It was commenced in 1863 and recommenced in 1865. By then the plans had been revised to allow for iron shields in the casemates and iron shields to protect five guns on the roof. By 1871 Fort Gilkicker was complete, except for its iron shields that protected the guns.
The guns were declared superfluous to requirements by the Owen Committee in 1905 and they were removed. the fort continued its life as a married quarter for Royal Engineers station nearby in Fort Monckton and at the R.E.
The fort was briefly used in WWII as a signal station relaying a vast number of messages to and from the Allied beaches in Normandy during Operation Overlord.
In 1956 all Coast defences were declared obsolete and the fort passed into the hands of the Ministry of Public Buildings and Works. It became workshops for a while. It was also used as a store for submarine parts as an extension to HMS Dolphin.
It was finally declared superfluous by the Military and was bought by Hampshire County Council in 1986. The intention was to convert it for modern use as high quality apartments. It was used briefly as a store for building materials but continued to decline, although it had been made an Ancient Monument and a Listed Building in an attempt to preserve it from unsympathetic development or complete destruction.