The integration of clinical data offers significant potential for the development of personalized medicine. However, its use is severely restricted by the General Data Protection Regulation (GDPR), especially for small cohorts with rare diseases. High-quality, structured data is essential for the development of predictive medical AI. In this case study, we propose a novel, multi-stage approach to secure AI training: (1) The model is designed on a simulated clinical knowledge graph (cKG). This graph is used exclusively to represent the structural characteristics of the real cKG without revealing any sensitive content. (2) The model is then integrated into the FeatureCloud (FC) federated learning framework, where it is prepared in a single-client configuration within a protected execution environment. (3) Training then takes place within the hospital environment on the real cKG, either under the direct supervision of hospital staff or via a fully automated pipeline controlled by the hospital. (4) Finally, verified evaluation scripts are executed, which only return aggregated performance metrics. This enables immediate performance feedback without sensitive patient data or individual predictions, leaving the clinic. A fundamental element of this approach involves the incorporation of a cKG, which serves to organize multi-omics and patient data within the context of real-world hospital environments. This approach was successfully validated during the TUM.ai Makeathon 2024 (TUMaiM24) challenge set by the Dr. von Hauner Children's Hospital (HCH-LMU): 50 students developed models for patient classification and diagnosis without access to real data. Deploying secure algorithms via federated frameworks, such as the FC framework, could be a practical way of achieving privacy-preserving AI in healthcare.