The absence of adequate national strategies for rare diseases (RD), high medicines prices and insufficient experts' knowledge creates to the barriers in therapy, as well as the added factors of inappropriate diagnostics and difficulties in peoples' access to health care. A heavier burden is placed on patients' physical, mental, psychological and intellectual wellbeing as well as on the financial capabilities of the third party payers. This study aims to analyze the financial flow for RD therapy as part of the health insurance budget and regional differences in their financing. The point of view is that of the third party payer for a 4-year period. The study is a macro costing top down financial analysis of the expenditures for medicines for rare diseases spent by the 3rd party payer, in Bulgaria that is the national health insurance fund (NHIF). Applied were financial and statistical analyses towards the budget data for expenditures for pharmaceuticals at national and regional level. Results show a constant rise in healthcare medicines expenditures, including those for rare diseases therapy from 20 to 27 million € for a three-year period but it is not above 10% from the budget for medicines due to regulatory restrictions. A variety of deviations exist among regional counties, accounting for more than 50% differences in payment per diagnosis. This could be explained with insufficient knowledge and lack of therapeutic standards. There is a need for collaboration on a European level and the creation of a global fund to be able to satisfy therapeutic needs. A closer look at national differences and regional therapy is necessary, as well as standardization of health care services for better health care expenditures management.