Abstract—The increased demand of infrastructure projects is a decision-making problem faced by Indonesia. This is mainly related to the challenges that exist in the process of infrastructure project selection and prioritization. Thus, this paper aimed to understand the challenges of infrastructure project selection and prioritization faced by the largest economy in Southeast Asia. It took a case study approach from three different ministries that manage infrastructure project planning and development. Eighteen semi structured expert interviews were conducted to identify six categories of challenges from the current decision-making practices, namely: planning-related, programming-related, resources-related, behavior & coordination-related, policy & political-related, and regulatory-related challenges. Furthermore, this paper has also established the infrastructure development planning hierarchy as observed in Indonesia. In brief, this paper reflects the current decision-making practices regarding infrastructure project selection and highlights the importance of identifying the various challenges that exist in the current practices.