This study intended to develop an understanding about Smart Cities by investigating into the literature on the system thinking theory and on Smart Cities. We will thus use insights from the system thinking theory in an empirical research incorporating observations and interviews of researchers and practitioners, constructing two cases studies to respond to our research question: How can system theory be applied to analysis and comparison of the recent phenomena Smart Cities? This study was based on empirical study analysis including interviews and field observations conducted in international cities such as Fujisawa and Vienna. Those cities were treated as cases and a comparative case study analysis was conducted accordingly. The stress was put on their core goals and organizations. Smart Cities can be considered as systems under the system thinking theory. Vienna and Fujisawa SST are among them as they fit the systems’ characteristics. While comparing the two Smart Cities, one can notice few similarities and significant differences concerning their location, their main approaches, their methods of management and their financial structure. The concept can be applied to analyze many Smart Cities worldwide relevant in terms of size and conditions. City Halls or Companies involved in that field may be able to utilize some recommendations while building their Smart City initiative. The topic of Smart City is contemporary. As any new subject, it remains to the responsibility of academic researchers to build proper and detailed academic researches to develop theories and models to apply in businesses and organizations. The matter is also crucial to face climate change while keeping high human standard quality of life.