The analysis of global epidemics, such as SARS, MERS, and COVID-19, suggests a hierarchical structure of the epidemic process. The pandemic wave starts locally and accelerates through human-to-human interactions, eventually spreading globally after achieving an efficient and sustained transmission. In this paper, we propose a hierarchical model for the virus spread that divides the spreading process into three levels: a city, a region, and a country. We define the virus spread at each level using a modified susceptible–exposed–infected–recovery–dead (SEIRD) model, which assumes migration between levels. Our proposed controlled hierarchical epidemic model incorporates quarantine and vaccination as complementary optimal control strategies. We analyze the balance between the cost of the active virus spread and the implementation of appropriate quarantine measures. Furthermore, we differentiate the levels of the hierarchy by their contribution to the cost of controlling the epidemic. Finally, we present a series of numerical experiments to support the theoretical results obtained.