Healthcare sector expenditures persistently rise due to various public health, demographic, and socio-cultural reasons. This fact caused repeated calls for reforms of the economic model in the healthcare sector due to increased concern for efficiency. The aim of this paper is the comparison of the Slovenian and Croatian healthcare systems, focusing mainly on the current development stage and the future challenges of the management (cost) accounting systems. The research is mainly interested in the analysis of capabilities of cost tracking according to different criteria and identification of the main constraints in the implementation of a full costing method in Slovenian and Croatian hospitals. The methodology of the literature review and electronic survey was used to assess the practice in both countries. Analysing the data collected from the responses of 26 (100%) Slovenian and 52 (91.22%) Croatian hospital accountants and financial officers, it is possible to claim that Slovenian and Croatian management accounting systems are at a very early development stage. Nevertheless, the analysis reveals several similarities, as well as differences, between the two systems, and it can be concluded that Slovenia has succeeded in making greater progress, especially when observing systematical cost monitoring and implementation of national cost analysis.