The system of public universities plays an important role in the socioeconomic development of each country. In Vietnam, public universities perform a leading role in the national higher education system’s operation and development. Therefore, public universities are assigned funds, assets, and facilities to implement goals and prioritize investment policies in the country’s education and training. However, to appropriately allocate funding, the state must reconsider the performance of the public education system. This paper presents a methodology to evaluate the operating performance of public higher education in Vietnam. The research design model includes cluster analysis and ANOVA, and Duncan post hoc tests have been used to provide an overview of public universities’ current state in Vietnam and to identify each of the strengths and weaknesses in cluster-specific groups. Based on this study’s results, educational administrators can develop a reasonable financial budget allocation plan for each university cluster.