The Kawaiahaʻo mission began in 1820, one of the earliest Protestant footholds in the Hawaiian Islands. Four thatched churches preceded the coral structure, each outgrown or worn out in turn. The stone church was commissioned by the regency of Kaʻahumanu and designed by Reverend Hiram Bingham in the severe New England Congregational style the American missionaries had brought with them across the Pacific. Its construction coincided with a rival project: the Cathedral of Our Lady of Peace, built by the Roman Catholic Apostolic Vicariate of the Hawaiian Islands. That cathedral broke ground in 1840 and was substantially completed in 1843, just one year after Kawaiahaʻo's dedication. The two churches rose within blocks of each other, a stone-and-coral proxy for the denominational competition that shaped nineteenth-century Hawaiian Christianity.

Kawaiahaʻo Church became the spiritual heart of the Hawaiian monarchy. Kamehameha III, Kamehameha IV, Kamehameha V, and Kalākaua all took their constitutional oaths of office within its walls. State funerals and royal baptisms were held here, and the aliʻi — the Hawaiian ruling class — claimed the church as their own, earning it the nickname "the Aliʻi Church." Today, twenty portraits of Hawaiian royalty line the upper gallery of the sanctuary. King Lunalilo, who specifically requested burial in a church cemetery rather than the Royal Mausoleum, rests in a crypt near the front courtyard alongside his father. The church was so central to Hawaiian governance that losing it felt like losing a piece of the kingdom itself.

The relationship between Kawaiahaʻo and the monarchy was complicated by faith itself. Kamehameha IV and his wife Queen Emma were drawn to the Anglican tradition and established the Church of Hawaiʻi, commissioning the Cathedral Church of Saint Andrew as a new center of royal worship. Later monarchs — Kamehameha V, Kalākaua, and eventually Liliʻuokalani — preferred the Anglican cathedral. Yet Kawaiahaʻo never lost its hold on Hawaiian national identity. Princess Liliʻuokalani had directed the church choir before ascending to the throne. When she died in 1917, her body lay in state at Kawaiahaʻo Church for a full week before the funeral was held at ʻIolani Palace. Even after the monarchy was gone, the church remained the place where Hawaiʻi said goodbye to its last queen.

Kawaiahaʻo Church was designated a U.S. National Historic Landmark in 1962, along with the adjacent Mission Houses, as the Hawaiian Mission Houses Historic Site. But the building's significance is not frozen in museum status. Services continue every Sunday, and the Hawaiian language threads through the liturgy and hymns — a practice that connects the congregation to the church's founding era, when Hawaiian was the language of governance, worship, and daily life across the islands. Among the notable figures buried or memorialized on the grounds is Henry Berger, the Prussian-born bandmaster of the Royal Hawaiian Band, and Abraham Akaka, whose pastorate from 1957 to 1984 is remembered for his role in the American civil rights movement. The church is part of the United Church of Christ, denominationally far removed from the Congregational missionaries who built it, yet carrying their legacy in every coral block.