There is still no consensus on the definition of urban governance, which can be attributed to gaps in its empirical foundation across both time and space. The Austro-Hungarian Monarchy (1867-1918), with its complex state structure, serves as an ideal historical and geographical subject for unveiling aspects related to the birth of modern urban governance within a Central European context. To conduct comparative research, this study examines selected cities from two territorial autonomies of the empire: Zagreb, Osijek, Varaždin, and Zemun from Croatia-Slavonia, and Lviv and Cracow (Krakow) from Galicia. Urban governance within territorial autonomy, particularly from a historical standpoint, is a unique subject that lacks a substantial presence int he literature of urban studies and territorial autonomy. In this paper, an analytical framework was developed based on the key components of the transformation thesis of urban governance and metagovernance theory. The findings of the study indicate that the process of designating territorial autonomies and the various political factors behind them significantly shaped the formation of urban governance systems.