Crathes sits on land given as a gift to the Burnetts of Ley family by King Robert the Bruce in 1323.
In the 14th and 15th centuries the Burnett of Leys built a fortress of timbers on an island they made in the middle of a nearby bog. This method of fortification, known as a crannog, was common in the Late Middle Ages. Construction of the current tower house of Crathes Castle was begun in 1553 but delayed several times during its construction due to political problems during the reign of Mary, Queen of Scots.
It was completed in 1596 by Alexander Burnett of Leys, and an additional wing added in the 18th century. Alexander Burnett, who completed the construction of Crathes, began a new project, the early 17th-century reconstruction of nearby Muchalls Castle. That endeavour was completed by his son, Sir Thomas Burnett. Crathes Castle served as the ancestral seat of the Burnetts of Leys until Sir James Burnett, 13th Baronet gave it to the National Trust for Scotland in 1951. A fire damaged portions of the castle (in particular the Queen Anne wing) in 1966. Another historically important structure in this region linked to the Burnett of Leys family is Monboddo House.