The COVID-19 pandemic has severely tested humanity, revealing the need to develop and improve the medical, economic, managerial, and IT components of vaccine management systems. The vaccine lifecycle includes vaccine research and development, production, distribution, and vaccination of the population. To manage this cycle effectively the proper organizational and IT support model of the interaction of vaccine lifecycle management stakeholders is needed—which are an innovation ecosystem and an appropriate virtual platform. A literature review has revealed the lack of methodological basis for the vaccine innovation ecosystem and virtual platform. This article is devoted to the development of a complex approach for the development of an innovation ecosystem based on vaccine lifecycle management and a virtual platform which provides the data exchange environment and IT support for the ecosystem stakeholders. The methodological foundation of the solution, developed in the article, is an enterprise architecture approach, CALS technologies, supply chain management and an open innovation philosophy. The results, presented in the article, are supposed to be a reference set of models for the creation of a vaccine innovation ecosystem, both during pandemics and periods of stable viral load.