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As far back as 1842 there was a rough attempt at guiding ships into Wellington harbour when a beacon was erected on Pencarrow headland, then known as "Beacon Head". In the years to 1859 other beacons were erected, on both sides of the heads. In 1849 a shed was built from which the light of an ordinary lamp was exhibited from a bow window facing to seaward.

           In 1852 there were representations for a proper light to be installed but rising costs delayed approval and it was not until July 1857 that a tender was accepted for the casting in steel of a lighthouse from Messrs Cochrane and Company of Woodside Iron Works, Dudley, UK.

           On 21 June 1858 the lighthouse arrived in Wellington on board the barque Ambrosine in 480 packages, but it wasn't until September 1858 that the brigantine Caroline transferred the packages to Pencarrow Head, where they were hauled up to the lighthouse site. 

           On 1 January 1859 the Pencarrow light commenced operation and the first keeper was Mrs Mary Bennett, widow of the first Lightkeeper. In September of that year the eclipsing light mechanism was replaced with a fixed light.

           Control of the lighthouse was transferred from the provincial government to the Marine Board in 1863. In 1865 the lighthouse and reserve were brought by the Government from the Wellington Provincial Council.

           An explosive-type fog signal was established on 11 July 1898 and continued in use until 1927, when it was replaced by a compressed-air diaphone signal.

           Owing to the fact that on occasions fog would obscure the light while visibility at water level remained practically unimpaired the Wellington Harbour Board installed a suplementary low level automatic light at the bottom of the Pencarrow cliffs. This light became operational in September 1906, and continued to be the main approach light to Wellington for 76 years.

           In 1930 a tower was added to the low level light base, and the light enclosed at the top of the tower.

           Many shipwrecks occurred in the vicinity of Pencarrow, the largest being the SS Devon of 3934 tons which stranded below Pencarrow lighthouse on 25 August 1913 and subsequently became a total loss.

           The use of the light at Pencarrow was discontinued in 1935 when Baring Head lighthouse, about six miles to the south, became operational. Personnel were retained to operate the fog signal apparatus until 1960 when the Wellington Harbour Board installed a remotely controlled automatic fog signal on the low level light tower.

           In 1959 the old tower was declared a Historic Place by the recently formed National Historic Places Trust under the Historic Places Act 1954. However, it wasn't until late 1966 that the lighthouse was transferred from the Marine Department to the then renamed New Zealand Historic Places Trust (NZHPT).

           In 1960 the land was transferred from the Marine Department to the Department of Lands and Survey. Then in 1979 the lighthouse was included in a historic reserve of 2044 square metres. NZHPT was appointed to control and manage the reserve.