The exact date of foundation is not known, but historical documents indicate that Christian III of Denmark in 1540 gave the school a wing of the old Holy Ghost Monastery in Aalborg after the dissolution of the Danish monasteries. For many years the church was an integral part of the school but in 1814 it moved from the monastery buildings in Jomfru Ane Gade. In 1886-1889 the school moved to its current location in a newly built school in Sct. Jørgens Gade (orig. Saxogade), designed by V.Th. Walther. The school was rebuilt during 1924-1926 by Einar Packness and expanded 1959-1960 by Leopold Teschl
The school has since been expanded several times, including in the 1980s, when the sports hall and science wing was built. Recently, a completely new building was built with 10 new classrooms, so that the school is now better equipped to meet the new teaching methods, which are a part of secondary education and higher preparatory reform. The school's main building is newly refurbished including a library and study centre on the ground floor.
There are about 80 teachers at Aalborg Cathedral School and approximately 760 students who are assigned to 24 high school classes and 6 Higher Preparatory Examination (HF)-classes.