In 1856, Rev. Dr. James Nish of Beechworth conducted the first Presbyterian service in Benalla. On 28 November, 1865, Rev. Robert McCully was appointed at the first Presbyterian minister for Benalla and Mansfield. The following year, a small Neo-Gothic church was built on Church Street, at the northern end of Mair Street. A manse was built next door in 1870 and a vestry was added to the church in 1871.
Rev. McCully was succeeded by Rev. Alexander Murdoch (1868-1882) and Rev. Alexander McConnan (1884-1926). By 1901, the building could not accommodate the whole congregation, so in 1905, Rev. McConnan oversaw the building of the present, larger church. The Fincham pipe organ was installed in 1913 and enlarged the following year.
Rev. Reg Butchers arrived in 1926. More land was purchased in 1928 for a new manse, which was constructed in 1929 and occupied in 1930. Rev. Butchers remained until 1933 when he was called to Frankston. Rev. Raymond Simons succeeded him in 1933 and remained until being called to Williamstown in 1944.
Rev. Alistair McLean ministered from 1944 until being called to Bacchus Marsh in 1961. During this time, the old manse was demolished (in 1957) to make way for the new hall, which was completed in 1958.
Rev. Ken Melville came to Benalla in 1961 and remained until 1964, when he entered the Department of Christian Education.
In 1964, Rev. Stewart Chant was inducted. During his ministry, discussions were held regarding uniting with the Methodist church. Combined services were held in June 1966, alternating between the two buildings. When a formal vote was held in the 1970s, sufficient Presbyterians voted to remain out of the Uniting Church in Australia (which formed in 1977) for the property to be retained by the continuing congregation, though a significant number of members had joined the Uniting Church. At this time, the congregations of Thoona and Balmattum were joined to the Benalla Parish. Rev. Chant was instrumental in the continuing Presbyterian cause in the region, including assisting with the re-establishment of the Wangaratta Presbyterian Church.
In 1980, Rev. Chant retired to Queensland and was succeeded by Rev. Ken Martin. During his ministry, the Faith Mission Council was established and has continued to support mission work to the present day. After their time in Benalla was completed in 1989, Rev. and Mrs. Martin themselves went overseas as missionaries, going to Venda in South Africa.
Rev. Roy Taylor succeeded him at Benalla and remained until 1997. Rev. Dr. Dallas Clarnette succeeded him, initially as a temporary minister, and was inducted in 1999. In 2000, the parish hosted the General Assembly of the Presbyterian Church of Victoria. Dr. Clarnette retired in 2004.
The following years included a series of temporary ministries, including by Rev. John Mercer and Mr. Peter Stanton. In 2011, Rev. Ken Martin was again called as the minister of Benalla, and remained until January 2016, when Stephen McDonald was appointed as an exit student from the Presbyterian Theological College in Melbourne. He was ordained and inducted as the minister of the parish on 31st December 2016.