The existence of the Special Region of Yogyakarta in a historical context began with the history of the establishment of the Ngayogyakarta Hadiningrat Sultanate based on the 1755 Giyanti Agreement. . Kasultanan Ngayogyakarta Hadiningrat was founded in 1755 by Prince Mangkubumi with the title Sultan Hamengku Buwono I, while Duchy Pakualaman was founded in 1813 by Pangeran Notokusumo (brother of Sultan Hamengku Buwono II) who had the title Adipati Paku Alam I.
Since their establishment, both the Sultanate and the Duchy were royal governments recognized for their sovereignty. During the Dutch colonial era, the government in the Yogyakarta Sultanate was regulated by a political contract which was carried out in 1877, 1921 and 1940, between the Sultan and the Dutch Colonial Government. This shows that the Keraton does not just submit to the Dutch. The Dutch East Indies government recognized the Ngayogyakarta Hadiningrat Sultanate and the Pakualaman Duchy as kingdoms that had the right to regulate and manage their own governmental households known as zilfbesturende landschappen. The last political contract of the Ngayogyakarta Sultanate was listed in Staatsblaad 1941 Number 47, while the political contract for the Duchy of Pakualaman was in Staatsblaad 1941 Number 577.
During the Japanese occupation, Yogyakarta was recognized as a Special Region or Kooti with Koo as its head, namely Sri Sultan Hamengku Buwono IX. Under Kooti, ??structurally there were certain areas of government with officials.