After the global financial crisis of 2007-2009, multiple countries have faced tight budget constraints and slowdown in economic activity. In such conditions, OECD countries have started to pay more attention to implementing R&D programs aimed at boosting economic growth and social welfare. Emerging countries are also trying to collect best practices in this area for adapting the latter to national circumstances in order to ensure sustainable innovation development. The most promising examples of R&D policy tools are those used in the USA and EU. In this paper, we conduct a comparative study focused on the objectives of R&D programs in the USA and EU, the usage of particular tools for financial support of small and medium enterprises (SMEs), the development of public-private partnerships and international cooperation in such areas like creation and distribution of new technologies. If public funding of various fields of science in the EU is quite centralised within the specific large-scale framework programs, then such programs in the USA are less scaled, but much more focused and are related to particular areas like fostering R&D activities in small enterprises. Both the EU and the USA are actively developing international cooperation in the field of science and technology, including some collaborative projects with each other. We also analyze budgets and tools for public R&D funding in the private sector. There is an intensive use of various tools to enhance the creation of public-private partnerships as well as both direct and indirect instruments for R&D funding in the EU and the USA. We pay particular attention to managing R&D programs in terms of coordinating all stakeholders being involved. Our analysis reveals both the common and distinctive features of R&D programs as well as the most effective forms and best practices used in R&D programs in the EU and the USA.