St Joseph's Church, built in 1893, is part of the second Catholic Maori mission station established on the Whanganui River. It is closely associated with the religious order, the Daughters of Our Lady of Compassion and its founder Mother Mary Joseph Aubert (1835-1926). It is also associated with James K. Baxter (1926-1972), one of New Zealand's finest poets. In the early 1880s, partly due to the request of the local Ngati Hau to have their own priest, the site of Jerusalem (Hiruharama) was chosen by the Catholic Church in New Zealand as the spearhead of a rejuvenated Maori mission. The new mission was begun in 1883, and was led by the Marist missionary Father Christophe Soulas. Assisting him was Sister Mary Aubert and, for the first year, three sisters of St Joseph's of Nazareth. The first church (attributed to architect Thomas Turnbull), also known as St Joseph's (Hato Hohepa), was built on the site by local Maori in 1885, but was burnt down in 1888 by an irate Pakeha. At Jerusalem, Aubert was able to further develop her interest in traditional Maori medicine, producing her remedies for sale to support the mission. Aubert also founded a home to care for destitute and orphaned children. In 1892 (now) Mother Aubert founded the Daughters of Our Lady of Compassion, New Zealand's first indigenous religious order. The present church was erected at this time, with construction completed by April 1893.

The second St Joseph's was built in a simple Gothic revival style. Also by architect Thomas Turnbull, the design was not as elaborate as that of the previous church but its location on the hill above the settlement formed a striking landmark overlooking the Whanganui River. Its construction was largely funded by the efforts of Soulas and Aubert. Aubert and some of her fellow sisters undertook a journey around the country, often walking long distances, asking for donations to support the Jerusalem mission and raise money for the construction of the church.

Mother Aubert and three of her sisters left Jerusalem in 1899 to extend their work among the poor of Wellington, but the main Maori Mission remained. The school established by the mission was eventually closed in 1969. That same year the poet and social activist James K. Baxter, drawn by the blend of Maoritanga and Catholicism, established an alternative community at Jerusalem. Baxter, a devout Catholic convert, was known as Hemi at the settlement. The commune became the focus of adverse publicity and he left in September 1971. Baxter's experiences of Jerusalem were recorded in his books, Jerusalem Sonnets (1970), and Jerusalem Daybook (1971). Baxter returned to Jerusalem for a short time in 1972, but left for Auckland in August. It was during this later period that he completed his last book, Autumn Sonnets (1972). He died in October 1972, and was buried [on tribal land] at Jerusalem with a full Maori tangi - a rare honor for a Pakeha.

St Joseph's Church, Jerusalem, has great national and international significance. It is closely associated with the establishment of New Zealand's first indigenous religious order, the Daughters of Our Lady of Compassion and particularly its founder Mother Mary Aubert. St Joseph's remains a well-known and much loved landmark on the Whanganui River. The Sisters of Compassion, as they are more commonly known, have retained a strong presence in the Maori community, and the church is still used by the Order for services.