In 1848 the Basel Mission started a primary school at Kallai, near Calicut with about 11 pupils in five classes. This was the first school to teach English in Calicut and the school was known as the B.G.E.M. Anglo-Vernacular school. In 1859 the school was shifted from Kallai to the heart of the town (east of Mananchira) where the B.E.M. Girls High School stands now. As years went by, the school became more and more popular; in 1872 it was raised to a middle school.
Three years later, a new building was constructed for the school and, in 1878, the school was made a high school. G.T. Verghese was the first headmaster and under his management the school progressed rapidly. Since expansion of the classes was impossible in the existing building, in 1906 the school was shifted to the present building and the old building was handed over to B.E.M. Girls High school.