Moffat Academy traces its history to the local grammar school founded in 1639 by Dr Johnstone.

During the 1810s, the school entered a low period as there were suspicions that the funds endowed by Johnstone's estate were misused.

[2] On the 4th of March, 2024, First Minister Humza Yousaf and the Cabinet Secretary for Education and Skills Jenny Gilruth visited the academy to launch a new framework to combat gender-based violence in Scottish schools.

While there, Yousaf spoke to pupils on topics ranging from gender-based violence to misogyny, and was given a tour of the school by head teacher Tara Woods.

After the visit, Yousaf noted "I had heard a lot about the ethos and culture that’s being promoted within the school but I wanted to see it first hand and I’ve been blown away.