Finding new therapeutic uses for approved, off-patent or generic medicines could lead to safe, affordable and timely new treatment options for patients with high medical needs. However, due to a lack of economic incentives, pharmaceutical developers are rarely interested to invest in this type of research. Consequently, potential new uses for off-patent or generic medicines are mainly studied in independent proof-of-concept clinical trials initiated and led by researchers from academia, research institutes or collaborative groups. Yet, these researchers need additional financial support to conduct expensive phase III clinical trials to confirm the results from exploratory research. In this study, scientific and grey literature was searched to identify and evaluate new mechanisms for funding clinical trials with repurposed medicines. Semi-structured interviews were conducted with 16 European stakeholders with expertise in clinical research, funding mechanisms and/or drug repurposing between November 2018 and February 2019 to consider the future perspectives of applying new funding mechanisms. Traditional grant funding awarded by government and philanthropic organisations or companies is well known and widely implemented in all research fields. In contrast, the application potential of newer mechanisms to fund independent clinical research, such as social impact bonds or crowdfunding, is not yet known. Interviewees stated that there is a substantial need for additional financial support in health research, especially in disease domains where there is limited commercial interest. However, the implementation of new funding mechanisms is facing several practical and financial challenges, such as a lack of expertise and guidelines, high transaction costs and difficulties to measure health outcomes. Furthermore, increased collaboration and centralisation at a European and international level is recommended to make clinical research more efficient and reduce the need for additional funding. New funding mechanisms to support clinical research may become more important in the future, but the unresolved issues warrant further exploration in pilot projects.