Non-profit organizations play an important role in our lives, but they still face financial problems. The diploma thesis deals with the financing and operation of public institutions within the framework of the non-profit sector. With this research we wanted to show the main sources of funding for such organizations and explain the problems they deal with and also get a better understanding of the operation of the non-profit sector. A descriptive method was used for the main research method, with the help of which we analyzed professional literature with a selected topic, as well as annual reports and financial statements of the selected organization. Center za izobraževanje, rehabilitacijo in usposabljanje Kamnik, which deals with physically challenged children and adolescents, was discussed. We also compared it with a similar organization, as we wanted to find out what are the differences or similarities in the financing of two public institutions that operate in the same field. The research showed that the selected organization obtains most of the funding from the state budget, and that donations do not play a major role. We found that the Institute is facing a shortage of space, which prevents it from operating fully in certain areas, and the funds received by the Institute are not sufficient for immediate action. It is proposed that the Institute takes a larger initiative in the field of fundraising and betters the communication with the ministry in charge, which would speed up the resolution of matters. The research gives us an insight into the issues, operation and financing of the non-profit sector and public institutions and can act as a »tool« for possible further research.