The origins of St Joseph's Primary School extend far beyond the city of Lisburn, beginning as an idea in Béziers, France, with Fr. Jean Gailhac and the Order of the Sacred Heart of Mary.

In 1870, Dr. Patrick Dorrian, the Bishop of Down and Connor Diocese, invited the Sacred Heart of Mary sisters from Béziers to establish a convent. They promptly answered the call and, in 1871, occupied a three-storey house adapted for use as a convent. Within the convent, a room was converted into a classroom where the nuns educated a small number of girls from the Lisburn area.

In 1902, a grant-aided school, formally known as 'The Convent,' was built to accommodate 224 girls and officially became St Joseph’s Primary School. For the next 98 years, the Sisters of the Sacred Heart of Mary delivered quality education, with the first lay principal taking on the role in 2002.

The original building was replaced in the 1960s with the present structures, and the school became co-educational in 1965 accepting boys for the first time.

In 2024, St Joseph’s joined the Global Network of the Religious of the Sacred Heart of Mary, a worldwide collective of schools and colleges founded by the Sisters of the Sacred Heart of Mary.

St Joseph's Primary School's aims and values continue to align with the mission of Fr. Jean Gailhac and the Sisters' vision for education.