Higher education institutions are the strategic assets that enable a country to a hold strong competitive advantage in the modern technological era. Higher education system has dramatically changed due to the paradigm shifts brought by the twenty first century trends. Moreover, the COVID-19 pandemic has also changed the higher education system around the world. Due to such shifts, new performance standards have been created, and the higher education institutions across the globe including Southeast Asian region are facing different challenges. To explore these challenges a non-systematic narrative review of existing literature was carried out, which helped in examining the role of higher education in the modern era. Moreover, it also helped in presenting an overview of higher education system in the Southeast Asian countries by discussing the challenges experienced by it. Finally, this chapter has explored the options available for supporting the continual development of the higher education in the Southeastern Asia.