Clinical hospital centers and general hospitals represent the primary sources of debt in the Croatian health sector. In response to concerns about financial sustainability, the Croatian government will implement a significant organizational reform of the hospital sector in 2024. According to the provisions of the Healthcare Act, the management of general hospitals will be transferred to state ownership. In addition, a new Public Health Protection Network will be established, introducing structural and organizational reforms to centralize the planning of health resources based on regional (county) needs. The aim of this study is to examine the differences in the technical efficiency of hospital operations between counties and to identify trends over time. To this end, the Window Data Envelopment Analysis (WDEA) is applied to the period from 2016 to 2022. The results show significant differences in the efficiency of the healthcare system between the counties, which underlines the need for targeted measures and systematic monitoring. In this context, the new Public Health Protection Network is positioned as a strategic initiative to promote integrated, patient-centered care.