Background: Rare diseases (RD) often manifest with heterogeneous, multisystemic phenotypes in childhood and evolve as chronic conditions. The RD pose a challenge for all affected and involved people. Funded by the German Federal Joint Committee (G-BA) the Innovation Fund project TRANSLATE-NAMSE had the goal to develop and test patient pathways to improve care for people with RD. Objective: To develop a generic clinical pathway for patients with a presumptive diagnosis of one of five groups of RD that coordinates interdisciplinary care workflows from confirmatory diagnostics to long-term care of these patients. Methods: The clinical pathway was designed as a general flowchart and process steps were transferred into an itemized checklist. The pathway was field-tested in 587 cases with a presumptive diagnosis of defined rare diseases in six university medical centers. Results: A diagnosis was made in 369 (62,9%) cases with defined presumptive diagnoses and of those in 25,2% by innovative genetic testing. In 104 (17.7%) cases the presumptive diagnosis was discarded as false positive and 114 (19,4%) cases remaining unsolved. The median number of specialists attending case conferences was four. The median time between diagnosis and start of care (diagnosis, training, counselling, and information) was 0 days. Satisfaction of caregivers with the clinical pathway was high as shown by external evaluation. Conclusion: In the German TRANSLATE-NAMSE project a clinical pathway for children with a suspected rare disease was successfully developed and tested. Implementation of this pathway into standard care requires adequate financing.