Central to any medical domain is the challenging patient to medical professional assignment task, aimed at getting the right patient to the right medical professional at the right time. This task is highly complex and involves partially conflicting objectives such as minimizing patient wait-time while providing maximal level of care. To tackle this challenge, medical institutions apply common scheduling heuristics to guide their decisions. These generic heuristics often do not align with the expectations of each specific medical institution. In this article, we propose a novel learning-based online optimization approach we term Learning-Based Assignment (LBA), which provides decision makers with a tailored, data-centered decision support algorithm that facilitates dynamic, institution-specific multi-variate decisions, without altering existing medical workflows. We adapt our generic approach to two medical settings: (1) the assignment of patients to caregivers in an emergency department; and (2) the assignment of medical scans to radiologists. In an extensive empirical evaluation, using real-world data and medical experts’ input from two distinctive medical domains, we show that our proposed approach provides a dynamic, robust and configurable data-driven solution which can significantly improve upon existing medical practices.