The establishment of the Croatian Institute for Emergency Medicine started with the establishment of the Institute for Emergency Medicine in the Republic of Croatia. From the very beginning of their existence, the institute faces organizational financial problems. The purpose of this paper is to provide an empirical study of the various difficulties and problems of the Emergency Medical Service that they face in their everyday work. The conclusions of the research conducted are the basis for making recommendations for their solution and improvement. Of the 21 Emergency Medicine Institutes operating in the territory of the Republic of Croatia, ten Institutes were selected in the selected research. The sample frame was created according to the geographic criterion and size criterion of the Institute. For selected Institutes, the financial statements for the years 2015 and 2016 are analyzed according to the business characteristics: financial result, liabilities, receivables, short-term assets, employees and organizational structure in accordance with the contract signed by the institutes with the Croatian Health Insurance Institute. The results of the research have shown that most of the Institutes, even 90% of them, have a surplus of income over expenditures in both analyzed years. Although the income from the Croatian Health Insurance Institute accounts for approximately 90% of revenues, the surplus of income is the result of other sources of income: decentralized functions of equalization funds, miscellaneous and extraordinary income and revenues from other beneficiaries, largely consisting of counties, cities and various ministries. Revenues from the Croatian Health Insurance Fund contract with even half (50%) of the institutes are insufficient to cover the regular operating expenses and therefore to invest in new, more modern and quality equipment. With the help of the mentioned other sources of funding, the institutions have been provided with regular payments of liabilities. The Institute's analysis alone in this paper provides sufficient evidence for suspicion of the possibility of monitoring the constant increase in the costs of the contractual arrangements with the Croatian Institute for Health Insurance. With financial problems, research has shown that the Institutes are struggling with a lack of doctors also. The potential to solve the identified organizational problem is reflected in the creation and implementation of emergency medicine reform. Work has suggested guidelines that could serve as a basis for creating a new reform policy for the Emergency Medicine Institution, whereby doctors from the Institutes would be redistributed to a unified emergency response, and medical staff / medical nurses would take on a greater role and responsibility in the institutes. Overall, observing the health system in the Republic of Croatia, we can conclude that the future of emergency medicine and institutes as providers of this service is unquestionable.