St John's, Waihi School, was designed by noted Christchurch architect Thomas Cane and erected on a site in Winchester township by Temuka contractors Clinch and Lloyd. The nave of the church was consecrated by Bishop Harper on 25 March 1879. Cane's plans also provided for a chancel, spirelet and porch; but these were beyond the immediate means of the congregation. However provision was made for the removal of the east wall to allow for future additions. The chancel, porch and vestry were subsequently constructed by Mr Waters of Geraldine, and consecrated by Archbishop Julius on 7 June 1890 on his first visit to South Canterbury.

In the 1960s declining attendance at churches in Winchester led to the decision to unify the Presbyterian and Anglican parishes, with activity centred on the Presbyterian Church Hall. In 1971 the Anglican Parish offered their now redundant building as a gift to the Waihi Preparatory School, covering the cost of moving it to its new location, repairing and painting it. In June 1972 the church was shifted the few kilometres north to the grounds of the school, where it was formally reopened the following September. This enabled it to serve not only the parish, but also as chapel for the Anglican boys preparatory school.

The Waihi Boys' Preparatory School was established in 1907 by Joseph Robinson Orford, an English born teacher who had lived in New Zealand for some years, and who felt that the South Island needed a boys' preparatory school. He bought a 15 acre paddock of stony broom and gorse covered land just north of Winchester and built a large house to serve as his family home, with boarding accommodation and school rooms included. It opened in September 1907 with just three pupils, the numbers increasing as each year passed, but about 80 has been the ceiling. There were close links with St John's Anglican Church from the earliest days of the school with Orford conducting many of the services as the vicar from Temuka was only scheduled here once a month.

When Orford died in 1924 a memorial plaque was placed in the nave of the church, and the Waihi Old Boys Association commemorated him by providing the stained glass window, installed in the chancel in 1930. Designed and executed by Veronica Whall it is an unusual example of her superb craftsmanship in her use of soft pastel colourings rather than the more frequently seen rich, vibrant colour hues. Renowned in Canterbury for the quality of the windows she designed for churches in the province, the English artist has depicted "The Christ-Child Blessing in Majesty with Emblems of Faith and Hope." Painted around the enclosing arch are the words "Give unto the Lord the glory due unto his name. Worship the Lord in the beauty of holiness." As well as the memorial to Orford there is also a brass tablet commemorating local flour miller D. Inwood, benefactor of the church's original site.

In the 1960s the school's connection with the church lessened as State Highway 1 had become so busy it was hazardous for the boys to walk to church, and services were conducted in the school's music room. The donation of St John's Church overcame the school's need for a chapel of its own, while ensuring the heritage building's retention and continued use in its home town.

Thomas Cane (1830-1905) was born in Brighton, England, and worked for Sir George Gilbert Scott before emigrating to Canterbury in 1874. Cane initially succeeded Benjamin Mountfort as Provincial Architect in 1875, but became Education Board Architect following the abolition of the provinces in 1876. Buildings designed by Cane include the Lyttelton Time Ball Station (1876), the original Christchurch Girls' High School (1876), and the School Master's House, Timaru (1878).