From 1603 the town of Elgin had 2 schools – the Grammar school, sited on the corner of what is now Commerce Street, and The Sang School or English School situated on the lands of Maisondieu. 

In 1791 the Town Council of Elgin planned to bring the 2 schools together and form a new Academy which was built on the corner of Francis Place and Academy Street and was officially opened in 1801.  Due to the increasing roll, a new school was built in Moray Street and opened for use in 1886.  The roll of pupils outgrew this building, so work started on the present buildings at Morriston in 1964.  These were completed and opened in 1969.
 

Most of the pupils arrive at Elgin Academy in S1 (First Year). Many come from the vast selection of nearby primary schools such as Bishopmill Primary, West End Primary, East End Primary, Seafield Primary and St Sylvesters to name but a few. There are, however, many other pupils who have arrived in later years, mainly because of the nearby Royal Air Force bases at Lossiemouth and Kinloss.

The Elgin Academy Awards Ceremony is held annually at the beginning of the last week of term before the summer holidays begin.

The Dux of Elgin Academy
This award is presented to the sixth-year pupil with the best performance across all undertaken subjects.

The Dux of S5
This award is presented to the fifth-year pupil with the best performance across all undertaken subjects.

Merits
Merits are awarded for general good work and behaviour or sometimes for completing a more specific task. Merits are recorded in each pupil's student planner and on the completion of a set number of pages certificates (Bronze, Silver, Gold and Platinum) are awarded.