In 1963, The Rev. George E. Hall, Rector of Calvary Church in Flemington, identified the need for a new Episcopal Church to serve the growing community in northern Hunterdon County. The land on Haytown Road was purchased in August of 1965 and the first service of the Church of the Holy Spirit was held at Clinton Community Center on September 11, 1966, with 89 people in attendance. Fr. Eugene Loughran, Vicar, led the service.
Ground was broken at Haytown Road on July 6, 1969 and the first service was held at the new church on Whitsunday, May 17, 1970. Installation of the organ began on June 19, 1970, with the dedication of the new church taking place on June 24, 1970. In 1974, the congregation voted to request full parish status, and on May 7th of that year, the Diocesan Convention accepted Holy Spirit as a parish. The Reverend Walter F. Smith was installed as the first Rector on June 19, 1974.
In February of 1982, Winthrop Jones was retained as architect to design an extension of the building and by January of 1984, the building additon was dedicated.
Our present Rector, the Rev. Philip Carr-Jones, came to the Church of the Holy Spirit on September 9th, 1987. In September of 1996, the Parish agreed to go forward with plans for a new building to serve the needs of the ever-growing community. Ground breaking was on June 14, 1998 and construction began. The dedication of the new building took place on May 20, 2000.