The school was named in memory of Charles Mackenzie, a prominent figure in the early history of Malawi. He joined David Livingstone on the Zambezi in 1861 as Bishop of Central Africa and Head of the Anglican Universities Mission, the first Christian mission in this part of Africa and the inspiration of Livingstone himself.
Established in 1944 as The European School, BMIS has a historic background from colonial times. It began with just a few students at the Golf Club but saw substantial growth in the 1950s. The school moved to its current location and provided boarding facilities during the Rhodesia and Nyasaland Federation. It later transitioned to a day school under the Nyasaland Government. In 1977, boarding facilities were reintroduced with the Designated Schools Board.