Economic studies of vaccines, including vaccine development and delivery issues, are increasingly needed to inform policy recommendations and programmatic decisions in the USA. This need arises from the increasing costs of vaccines, the complexity of the US healthcare system and the limited number of vaccine manufacturers in the market. We have developed a national research agenda in domestic and global vaccine economics by conducting key informant interviews with 42 experts and inviting ideas from an additional 128 experts. To assess priorities among the 129 ideas that were generated, we asked 15 experts representing a broad range of perspectives to rank the ideas and we analyzed their votes. The highest-ranking domestic research ideas included evaluating: the costs of vaccine shortages, the cost-effectiveness of potential human papillomavirus vaccination and adult and adolescent pertussis vaccination programs and the cost-effectiveness of universal vaccine purchase programs for adults as well as children. The highest-ranking globally-oriented ideas included developing a resource allocation model to support the best vaccination program decisions with limited funds and assessing the cost-effectiveness of HIV, rotavirus, meningococcal and malaria vaccines in developing countries. To optimize the usefulness of vaccine economics research, conceptual issues, such as how to set values for the prevention of illness and how to maximize social equity through investments in vaccines, must be addressed.