Despite a constant number of prescriptions, the expenditures of the statutory health insurance funds for pharmaceuticals are rising sharply. This is due to high prices for orphan drugs and advanced therapy medicinal products (ATMPs). Despite attempts by policymakers to intervene, such as the 2011 German Pharmaceutical Market Restructuring Act (Arzneimittelmarktneuordnungsgesetz, AMNOG), the use of these therapies poses numerous challenges for the healthcare system, especially insurance companies and healthcare providers. Using data from the University Hospital Heidelberg, we found that the division of pediatric neurology is experiencing a disproportionate increase in drug costs, caused by two drugs for the treatment of spinal muscular atrophy (SMA), Nusinersen and Onasemnogen Abeparvovec. A survey of 41 German SMA treatment centers revealed a lack of human and infrastructural resources to manage therapy and follow-up care, which currently is insufficiently reimbursed. Disease-independent registers that comply with the rules of the European Union for medication surveillance and which are not tied to the pharmaceutical industry are necessary. Innovative forms of therapy require a critical discussion and regulation of application, aftercare and reimbursement as well as (inter)national industry independent registry work. Based on the model of evidence-based dynamic pricing by the Techniker Krankenkasse, we propose a concept which offers an internationally scalable solution to combat these challenges.