Introduction: One of the most successful approaches to treat patients with rare diseases in a quality, timely and effective manner is to create a rare disease ecosystem. It represents a functional environment that integrates all stakeholders, procedures, and relations required for organized and effective patient treatment. This paper explores the current situation in the field of rare diseases, especially in light of the proposed ecosystemic arrangement, and drafts a blueprint for the design of a rare disease ecosystem in Slovenia. \nMethodology: The research applies a case study design, where focus groups were used to assess the state of affairs, generate ideas, and collect evidence from the field. Structured discussions were conducted with eminent experts affiliated with the leading institutions in the field of rare diseases in Slovenia. Analysis and interpretations of the data obtained were carried out by means of conventional content analysis. \nResults: Setting up a rare disease ecosystem in Slovenia would render a significant advance for patients, as it could considerably promote the coordination of healthcare treatment and facilitate extensive monitoring of the treatment parameters and outcomes. A well-organized rare disease ecosystem could convey considerable systemic benefits to evidence-informed policymaking, better utilization of resources, technological innovation, and business processes reengineering. \nConclusion: Providing quality healthcare delivery in this complex field is largely reliant on the effective integration and collaboration of all entities within the rare disease ecosystem, alignment of related systemic factors, and the direction of healthcare services to support the needs and well-being of patients with rare diseases.