Rare diseases (RDs), with distinctive and complex features, pose a serious public health concern and represent a considerable challenge for the Slovenian healthcare system. One of the potential approaches to tackling this problem and treating patients with RDs in a quality and effective manner is to form an RD ecosystem. This represents a functional environment that integrates all stakeholders, procedures, and relationships required for the coordinated and effective treatment of patients. This paper explores the current situation in the field of RDs, especially in light of the proposed ecosystemic arrangement, and provides an outline for the design of an RD ecosystem in Slovenia. The research applies a case-study design, where focus groups are used to collect evidence from the field, assess the state of affairs, and generate ideas. Structured focus group discussions were conducted with preeminent experts affiliated with the leading institutions in the field of RDs in Slovenia. Analyses and interpretations of the obtained data were carried out by means of conventional content analysis. Setting up an RD ecosystem in Slovenia would lead to significant benefits for patients, as it could promote the coordination of healthcare treatment and facilitate extensive monitoring of the treatment parameters and outcomes. A well-organized RD ecosystem could garner considerable systemic benefits for evidence-informed policymaking, a better utilization of resources, and technological innovation. Delivering quality healthcare in this complex field is largely reliant on the effective integration and collaboration of all entities within the RD ecosystem, the alignment of related systemic factors, and the direction of healthcare services to support the needs and well-being of patients with RDs.