The Johanneum was founded by Johannes Bugenhagen, the spiritual representative of the reformer Martin Luther.

In 1528 he came to Hamburg to give the city an Evangelical Lutheran church order, "the Erbarn Stadt Hamborch Christlike Ordeninge".

On 24 May, 1529, the Johanneum first opened its doors in the building of the secularized old St. Johannis monastery, on the site of today's Rathausmarkt as the "Latinsche Schole".

From 1838 to 1840, the new building at the Speersort was finally built on the site of the cathedral demolished in 1806, where the germ cell of Hamburg once stood, the so-called Hammaburg.

The imposing classicist new building, designed by Carl Ludwig Wimmel (1786–1845) and Franz Gustav Forsmann (1795–1878), to be entered from the south through the main entrance, had two wing structures leading to today's cathedral street through arcades were connected.

The building was based on competing designs by Alexis de Chateauneuf (1799–1853) and Carl Ludwig Wimmel.

The patriciate of the city republic of Hamburg was brought up humanistically in the Johanneum, important scholars and authors of the early Enlightenment worked here (Hermann Samuel Reimarus, Barthold Heinrich Brockes, Michael Richey, Johann Albert Fabricius, and others), Georg Philipp Telemann and Philipp Emanuel Bach were cantors here, and this established a lasting tradition and reputation.

The old building was largely destroyed in the bombing raids on Hamburg in 1943, the remains (including an arcade) were removed for widening the streets in 1955 (the foundations were uncovered again in 2005 during archaeological excavations on the cathedral square).

[3] In 1948, three years after the end of the Second World War, a group of students from the Johanneum visited London.

Frederick Wilkinson, the headteacher of the Latymer Upper School, believed that only getting to know young people can bring about understanding, reconciliation and thus lasting peace in Europe.

It replaces the eight provisional classrooms built in container construction, which have been installed between the main building and the forum since summer 2008.

In addition, mathematics with the Pythagoras theorem forms a bridge between the ancient natural philosophers and the present day.

In Jules Verne's novel Journey to the Centre of the Earth, one of the main characters, Otto Lidenbrock, is a professor at the Johanneum.

The school has an alumni society called Verein ehemaliger Schüler der Gelehrtenschule des Johanneums zu Hamburg e.V..