The school was opened on 23 March 1902, with 13 students, by the Mill Hill Missionaries, and was the first post-primary boarding school in Uganda.
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Makerere College School is listed among Africa's top 100 schools and shares fame with other traditional schools such as Mengo Senior School, Namilyango College, Gayaza High School, Rainbow International School and Lincoln International to mention a few.
Around 1900, the Mill Hill Missionaries settled on the hill and begun to build Namilyango College, a prestigious middle and high school, intended originally to educate the sons of chiefs.