Effective exchange of health data is crucial in the modern healthcare landscape, most notably for advancing research and clinical care on rare diseases where patient populations are small and often geographically dispersed. While numerous approaches to health data exchange exist, substantial challenges persist in achieving convergence and selecting technologies that address the diverse requirements of stakeholders. The Joint Action on Integration of European Reference Networks (ERNs) into National Healthcare Systems (JARDIN) aims to tackle these issues by fostering alignment around shared solutions. To explore practical strategies for automating secure data exchange among healthcare providers, national registries, and ERNs, a hackathon was organised by JARDIN, inspired by the software-oriented “Bring Your Own Data” workshop format, which promotes the Findability, Accessibility, Interoperability, and Reusability (FAIR) of research resources. The event brought together over 50 experts from across Europe. Participants tackled three core challenges: data harmonization, querying, and the FAIR description of data services. Key proposed solutions included leveraging semantic models for data harmonization, adapting existing infrastructures for (federated) querying, and extending the FAIR Data Point (FDP) metadata model to better describe data services. This paper outlines the methodologies and outcomes of the hackathon. The findings presented herein provide insights for JARDIN’s future work in developing recommendations for a robust, scalable, and secure data exchange ecosystem for rare diseases.