The institution traces its roots to the early missionary work of the Dutch Reformed Church Mission in Malawi. In 1902, a teachers' training institution was established at Mvera to prepare teachers and evangelists for mission schools across Central Malawi. As the mission expanded, the college was relocated to Nkhoma and became known as William Murray Teachers' Training College, named in honour of Rev. Dr. William Hope Murray, a missionary whose dedication to Christian education, Bible translation, and community development greatly influenced the growth of the Nkhoma Mission and the present-day CCAP Nkhoma Synod.
For many decades, William Murray Teachers' Training College trained generations of teachers who served mission and government schools throughout Malawi, playing a significant role in shaping the country's education system.
Following reforms in teacher education, the teachers' training programme was phased out in 1979. To continue the institution's educational mission, CCAP Nkhoma Synod transformed the campus into a secondary school. The first Form One class was admitted in October 1979, marking the beginning of William Murray Secondary School. By 1982, the school had become one of the Synod's leading secondary schools.
Today, William Murray Secondary School continues the legacy of its founders by nurturing young men of integrity, faith, academic excellence, and leadership.