The Church of St John the Baptist is a well-preserved example of timber Gothic Revival architecture, built during the latter stages of Church Missionary Society (CMS) involvement in New Zealand. Erected in 1870-1871, it sits within one of New Zealand's earliest churchyards, which is associated with two previous churches built on the site in 1831 and 1839. The churchyard and early chapels formed an integral part of the CMS station at Te Waimate, which had been established in 1830 as the first inland mission in New Zealand. The station was important for conveying new ideas on farming, education and religion to Maori in the Far North and subsequently witnessed an early signing of the Treaty of Waitangi on the 10th February 1840 (see 'Te Waimate Mission House, Waimate North'). As one of the earliest churches in New Zealand, the first chapel was the location of the earliest known Pakeha church wedding in New Zealand (1831). By 1832, its surrounding churchyard was in use, with initial burials including those of missionary children. After the construction of a replacement chapel in 1839, the associated mission station was temporarily used as a college by Bishop George Selwyn (1809-1878) in 1843-1844, and subsequently as a headquarters for the British army during the first New Zealand - or Northern - War (1845-1846), after which it lost support among Maori. The station gradually fell into disrepair, with the last missionary school closing down in 1868.

The current church was built as a replacement for the dilapidated 1839 chapel, but on a smaller scale. Unlike the previous structures, it was created for a largely Pakeha congregation, who had increasingly settled in the region. Although administered by the London-based CMS, the building was erected at the same time as the mission district was formed into an Anglican parish. It was opened in April 1871 by William Cowie (1831-1902), the first Bishop of Auckland, who was responsible for a period of Anglican expansion in the Auckland Diocese. Built at a cost of £374 by Woolle & Company, the church comprised a nave, chancel and steeple, as well as a transept on its northern side. The architect is believed to have been Marsden Clarke, a son of the Waimate missionary George Clarke (1798-1875) and brother of the first incumbent of the church Archdeacon E. Clarke (1831-1900). Its Gothic Revival design was similar to other CMS churches built from the 1850s, (see 'St Paul's Church, Hairini' and 'St John's Church, Te Awamutu'), but incorporated a board and batten exterior like Anglican churches in Auckland of the so-called Selwyn style, named after Bishop Selwyn. The building differed from the 'chapel' form of its 1839 predecessor, but retained references to its missionary origins by incorporating a pulpit, doors and other timber from the previous church. A timber Sunday School building was erected in the churchyard a few years later, in 1877.

Both buildings survived the withdrawal of the CMS from New Zealand in 1892, having been transferred to the Anglican authorities in 1886. Modifications to the church interior included the installation of an organ imported from Bevington & Sons in London in 1885. In 1929-1930, a stone lychgate was erected to commemorate the centenary of the CMS mission. From 1942, the centre of church activities in the area moved to nearby Kaikohe, following the growth of that town. In the middle of the twentieth century, the Sunday School building was relocated from the churchyard to adjoining land between the church and Te Waimate Mission House. Servicing a small rural settlement, the church continues to be used for religious services, and retains most of its early fixtures and furnishings. The surrounding churchyard has been more substantially modified, but includes the graves of British soldiers killed in the first New Zealand War and those of prominent individuals such as George Clarke and his family. It contains both Maori and Pakeha grave markers and is surrounded by an 1878 picket fence.

The Church of St John the Baptist is significant for its links with the Church Missionary Society, and the organisation's later operations in New Zealand. It is important for reflecting the relationship between the CMS and the Anglican Church in the later nineteenth century, and an expansion of the Anglican ministry. The building is a product of important changes within colonial society, including the declining impact of missionary activity among Maori and the development of pastoral care for Pakeha settlers. It is connected with the lives of prominent individuals in New Zealand history, such as George Clarke and Bishop Cowie. It is also significant for its well-preserved interior - including an historic organ - which reflects nineteenth-century attitudes to liturgy, music and religion.

The surrounding burial ground is outstandingly important as one of New Zealand's earliest churchyards. Its grave markers and other elements contribute towards an understanding of burial, commemoration and other aspects of early colonial and later life. The site has considerable spiritual and symbolic value to both Maori and Pakeha, having been at the heart of Christian worship and commemoration in the district for well over 170 years. They are part of a broader cultural landscape, which incorporates other important structures, buried archaeological remains and historic trees, as well as wahi tapu. Closely associated structures include a Sunday School that originally stood in the churchyard, and the second-oldest building in the country - Te Waimate Mission House - which was used as the church vicarage in the later nineteenth century.