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Introduction Performance-based resource allocation (PBRA) programmes have been increasingly adopted by medical schools as a strategic mechanism to optimise funding distribution, align resources with institutional priorities—particularly the delivery of high-quality education—and improve educational outcomes. In an era of budgetary constraints and growing demands for transparency and accountability in higher education, PBRA programmes offer means to enhance efficiency, incentivise quality and strengthen educational performance. Despite their widespread implementation, significant knowledge gaps remain. Specifically, there is limited evidence regarding: objectives of PBRA programmes (RQ1), structural design and key components (RQ2, RQ3), effectiveness in achieving intended outcomes (RQ4), implementation challenges and enabling factors (RQ5)This study aims to address these gaps through a comprehensive evaluation of PBRA programmes in medical schools across Switzerland and Germany, drawing insights from key stakeholders. The overarching research question guiding this work is: What are the key elements of successful PBRA programmes in Central European medical schools?Methods and analysis We will conduct a qualitative cross-sectional study using semistructured interviews with PBRA programme managers or experts from medical schools in Germany that already have PBRA in place and Switzerland, where the existence of PBRA programmes is currently unknown. Interviews will be held online (eg, Microsoft Teams), audio-recorded and transcribed intelligent verbatim for thematic analysis. A previously piloted and validated interview guide will be used. Data will be analysed thematically following Kuckartz’s methodology, combining inductive and deductive coding, supported by NVivo (V.15). Themes will be identified, discussed and refined as a team, possibly using frameworks such as the Consolidated Framework for Implementation Research and the Joint Committee on Standards for Educational Evaluation standards, to ensure alignment with established theoretical models. Results will be reported according to the Consolidated criteria for Reporting Qualitative research.Ethics and dissemination The study complies with the Swiss Ethical Review Act, which exempts non-sensitive qualitative research from formal approval (REQ: 2024-01001). Following study commencement and before completion of data collection, the study was registered on the Open Science Framework DOI: 10.17605/OSF.IO/QBDF2). Results will be published in a peer-reviewed journal, presented at conferences and shared with participating medical schools to foster collaboration and innovation in resource allocation.