Immunization is one of the most cost-effective interventions in global health and has a crucial role in achieving 14 of the 17 sustainable development goals (SDGs). The issue of sustainable financing for new vaccines is particularly pertinent as Indonesia transitions away from extensive Gavi support towards a self-financing immunization system. As the current immunization system transitions, practical solutions must be found and applied to provide more flexibility in the budget for financing immunizations without sacrificing the current healthcare system’s needs. Despite the fact that economic evaluation studies are essential as an initial step to ensure financial readiness, the lack of reliable data is the first barrier to Indonesia’s journey toward a self-financing immunization system. To overcome this problem, standardization of data collection strategies and methodologies are required. In particular, Indonesia may have to explore other options to increase revenue for its immunization system, such as through general revenue from the central government, a sector-wide approach to financing, and a national trust fund. To deal with the tight immunization budget and its consequences, Indonesia also has to restructure its immunization system, which can be implemented through province block grants, insurance mandate and subsidy. Taking the potential of a COVID-19 vaccine into account, the Indonesian government should consider a number of costs and issues beyond the development and procurement of vaccines. The costs of delivering vaccines to the remote parts of Indonesia, implementing the necessary infrastructure, and modifying vaccine delivery are also important in this time of transition. These constraints must be addressed in the new self-financing system and other public health efforts must be increased to decrease the burden of infectious disease as Indonesia develops a stronger immunization system.