, the first Bishop of New Zealand, purchased part of the site of the church in 1845 and Governor George Grey added to it in 1853, at which time the land stood on a prominent cliff-top overlooking Wellington harbour. Agreement to build the church was reached by 1861 and the ReverendFrederick Thatcher, then vicar of St Paul's, Thorndon, was engaged as the architect. The foundation stone was laid by Governor Grey on 21 August 1865. The building work was executed by John McLaggan and a team of eight carpenters, and the church was consecrated by Bishop Abraham on 6 June 1866. Soon after the church opened, it became apparent that it was unstable in high winds, and so the south transept, designed by Christian Julius Toxward, was added in 1868. Later additions included the north transept and north-aisle extension, also by Toxward, in 1874; the moving of the chancel five metres to the east and the addition of minor north and south transepts to the design of George Fannin in 1876; the choir vestry in 1882, probably designed by Toxward; and extension of the baptistry as designed by Frederick de Jersey Clere in 1891. Thatcher’s original wooden shingle roof was replaced with corrugated iron in 1895, and subsequently with Welsh slates in 1924. In 1964 the Diocese of Wellington moved to the new St Paul's Cathedral nearby. After a significant battle to prevent its demolition, Old St Paul's was purchased by the New Zealand Government in 1967, and subsequently restored by the Ministry of Works under the guidance of Peter Sheppard.
Old St Paul's is now managed by Heritage New Zealand Pouhere Taonga. While no longer used as a parish church, it remains consecrated, and is a popular venue for weddings, funerals and other services. The flags displayed in the nave include the ensigns of the Royal Navy, the New Zealand Merchant Navy and the United States Marine Corps, which was stationed in Wellington during World War II. The church retains close links with the New Zealand Defence Force. Some of the walls and columns of Old St Paul's are decorated with memorial plaques, including many dedicated to those who fought and died in World War I. There is a plaque in memory of Wellington historian John Beaglehole, most famous for his biography of explorer James Cook, but who also played a significant role in the fight to save Old St Paul's from demolition. Old St Paul's is closed from May 2019 until July 2020 for seismic strengthening work.