The name Academy refers to the school that Plato founded just outside of Athens near the temple of Academos, a hero of the Trojan War, in 387 BC. This name was brought back into use in Italy in the 15th century, when scholars came together and formed discussion groups around mainly three fields: philosophy, language and science. Among other things, they wanted to approach nature, conceived of as a coherent cosmos, in an experimental way, free from handed-down, mostly erroneous ideas. This gave a fresh impetus to the methodology for acquiring insight and knowledge and led to the advent of modern science. Academies for science were founded in Rome (Accademia dei Lincei, 1603), London (Royal Society, 1660), Germany (1652), Paris (1666) and finally also in Brussels (1772), in particular the Imperial and Royal Academy of Science and Letters of Brussels, during a period in which the Southern Netherlands was governed by  the Austrian Empress Maria Theresia. The latter Academy, however, was abolished when the Southern Netherlands was incorporated into the French Republic. It was re-established in 1816 by William I, king of the United Kingdom of the Netherlands, and was expanded with a department of the arts in 1845, fifteen years after the Kingdom of Belgium was established. During this first period, the Academy was accommodated in a number of rooms at  the Royal Library, now known as the Palace of Charles of Lorrain. The Palace of the Academies was originally the home of crown Prince William of Orange and his wife Anna Pavlovna. It was erected in Neo-Classical style between 1823 and 1828, according to the plans of architect Charles Van der Straeten, who was later succeeded by Tilman-François Suys.

Meanwhile, a separate Academy of Medicine was created in 1841. Those Academies were, of course, mostly French-speaking, and the advocates of the Flemish movement sought to establish a Flemish Academy. Their perseverance paid off 45 years later with the establishment of an Academy of Dutch Language and Literature in Ghent in 1886. It took until after the First World War before Dutch began to be used as language of instruction in Flemish higher education, first at Ghent University in 1930.  After a difficult struggle, in which a lot of resistance from the French-speaking intellectual elite had to be overcome, Flemish Academies were finally established in 1938: one  for Science, Letters and Fine Arts and one  for Medicine. This, however, created a confusing situation with on the one hand national, officially bilingual Academies, whose members came from the north and south of the country and on the other, Flemish Academies. In 1971, this was brought to an end by the creation of two equivalent Academies, a Dutch-speaking one, belonging to the Flemish Community and a French-speaking one, belonging to the French-speaking Community. The Academies for Medicine underwent exactly the same procedure. They are all under the same roof: the prestigious Palace of the Academies located at  Hertogsstraat 1 in Brussels.