St Matthew Academy opened in September 2007. The new Academy replaced two previous schools: St Joseph's Academy secondary school and Our Lady of Lourdes primary school. It was built on the site of the previous school's playing fields, with the St Matthew Academy playing fields created in turn on the site of the old St Joseph's buildings. The new Academy was built as a completely new state of the art school at a cost of £38 million budget.

St Joseph’s Academy was an all-boys Roman Catholic academy, founded in 1860 as an extension of the work of the De La Salle Brothers at St Joseph’s College, Clapham - a school in St George’s Parish, Kennington. The Brothers who originally taught in the Academy initially belonged to the Clapham Community and travelled each day to Kennington.  It became a separate school in 1865 and operated in Kennington for 56 years. In 1916 it moved to Camberwell, and finally it moved to Lee Terrace in 1919 to become St Joseph’s Academy, Blackheath. In 1977 St Joseph’s Academy made the transition from grammar school to comprehensive school. St Austin's Boys School, Charlton merged with St Joseph's Academy in the early 1980s and for some time the St Austin’s site was used for the lower school. Eventually, the site in Charlton was repurposed as the site for Christ the King Sixth Form College before it moved to its current site on Belmont Hill.

In 2007, St Matthew Academy formed one of the original academies created under the then Labour government to replace failing schools. The results in the final year of the old secondary school of just 26% of year 11 students gaining at least 5 A*-Cs (including English and Maths) in their GCSEs improved quickly to reach nearly 60% in 2014. After slipping back somewhat in 2015, the results are back up again near 60%, with expectations in 2017 and beyond of further increases. Similar trends have been seen in the key measures in the primary phase of the Academy.

The school's original Principal, Monica Cross, was followed on her retirement in 2012 by Michael Barry, who in turn was succeeded in 2016 by our Current Head of School, Miranda Baldwin.