The church was established in 1885 by King George Tupou I (formerly Taufa'ahau Tupou I) and Rev. Shirley Waldemar Baker with its goal being independence from Methodism in Australia, with Tonga having its own control over properties and assets. Originally with the name The Free Church of Tonga, it became the official state church. Queen Salote and King Tupou IV were both christened in the Free Church of Tonga. There was an attempted re-unification in 1924 by the Wesleyan Mission and Her Majesty Queen Salote after marrying Prince Consort Viliami Tung? Mailefihi (a Methodist follower), to unite Free Church of Tonga with the Methodist church. An emergency church conference called by Queen Salote at the Royal chapels in the palace grounds in Nuku'alofa to join the two congregations together was unsuccessful, ending with a "walkout" by the then-president of the Free Church of Tonga. This left all the properties and assets to the Free Wesleyan Church of Tonga (later established by Queen Salote). With less attention to properties and assets loss, J.B. Watkins (who had been president since it was established), the Reverend Paula Fonua and all their ministers continued to sustain the church. It was first presided over by foreign ministers until the presidency came into local hands, the Fonua family, where it has stayed since.
To date, the Free Church of Tonga has church groups and members in Tonga, New Zealand, Australia, America, Fiji and American Samoa.
The church operates three high schools, one each in Tongatapu, Ha?apai and Vava?u, all named Tailulu College. The church also operates two pre-schools in Auckland, New Zealand - Falemasiva and Lou'olive. The church is obligated with the heavy task of running the schools. About 20% of church funds are spent on education.
The church has an administration centre at the outskirt of Tonga Central Business District. The church have its own Constitution, and also holds an annual conference. The current Leader of the Free Church of Tonga is its president, the Reverend Semisi Fonua, who has been President since the Church Conference of 1984, replacing his father, the late Reverend Kisione Lelea Fonua. They are descendants of the Reverend Paula Fonua. The post of the president is elected annually during church annual conference.