The Junior Academy was established in 1988 to provide a supportive smaller school setting in which both boys and girls could participate in an elementary school program that stressed individual excellence and a high level of academic achievement. Although the Junior Academy opened with a single primary class for students aged 6 to 8 years old in September 1988, it gradually grew until it offered classes from Kindergarten to Grade 6. In 1996 the acquisition of its own premises enabled the Junior Academy to expand further and add on Grades 7 and 8.

Previous administrative positions held by Mrs. Johnson include a seven year term as the Director of the Junior School at Miss Edgar's and Miss Cramp's School in Montreal and a four year term as the Principal of Montcrest School in Toronto. Miss Edgar's and Miss Cramp's is a university preparatory school for Girls from Kindergarten to Grade 12 and Montcrest is a co-educational school for students from Junior Kindergarten to Grade 8 whose programs include special education classes for children with learning disabilities. Both of these schools were originally established in keeping with the tradition of the smaller independent school: a tradition to which Mrs. Johnson chose to renew her commitment when she became the founding principal of the Junior Academy.