In the national project TRANSLATE-NAMSE funded by the German Federal Joint Committee, a patient pathway for transition of people with rare and ultrarare diseases from pediatric to adult care was successfully developed and implemented. A total of 292 patients with a rare disease (median age 17 years, interquartile range, IQR 2.0 years) completed the pathway between 2018 and 2020. The patient pathway was characterized by 1. an assessment of patients state of knowledge, 2. targeted briefing and training by the pediatric specialists/teams, 3. the completion of a transition epicrisis and 4. joint consultation with the adult specialist/treatment team. Administrative tasks, including scheduling of appointments, was carried out by the patient coordinator from the associated centers for rare diseases. The data of this large nationwide cohort enables for the first time a calculation of the necessary resources and costs in the German healthcare system for a structured transition program. For the coordinative tasks (patient coordinator) a mean of 84.70 €± 29.90 € (mean ± SD)/case incurred. A median of 2 (min/max 1–5; IQR 2) clinic consultations with training sessions were carried out by a median of 3 (min/max 1–7) people (doctors, nurses, dieticians, etc.) involved. The average costs for each per patient during the transition process in the participating clinics were 157.70 €± 83.00 € (mean ± SD) and on average 599.00 € ± 380.50 € for all clinic appointments during the process. The results show that a structured and high-quality patient pathway for transition can be achieved even for patients with rare diseases by the cooperation with the specialized pediatric and internal/neurological care providers and inclusion of the local centers for rare diseases and with manageable costs.