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Introduction: Kosovo and Croatia share a common regulatory and historical background, yet their pharmaceutical systems have developed along different trajectories. Croatia’s EU membership and strategic investments have enabled full regulatory integration, while Kosovo continues to face structural and institutional challenges despite aligning its legal framework with EU standards. Key differences are evident in marketing authorization procedures, medicine availability, and regulatory implementation. Thus, this study highlights these gaps that Kosovo must strengthen and adopt EU-aligned best practices. Objectives: This study aims to analyze Kosovo’s current pharmaceutical regulatory system, particularly its alignment with EU standards, using Croatia’s well-established system as a benchmark. In addition, the aim of this paper is to evaluate the marketing authorization procedures in Kosovo compared to Croatia and also assess the availability and diversity of marketing-authorized medicines in both countries. Furthermore, a key focus area is the availability of New Molecular Entities in both countries and identifying the gaps in Kosovo’s pharmaceutical market. Materials and Methods: A comparative and analytical approach to the pharmaceutical regulatory framework of Kosovo and Croatia is used in this study. Data were collected from national and EU legislation, and the official regulatory agency databases from September 2024 to January 2025. Data were analyzed using thematic content analysis to identify regulatory themes and a quantitative comparison to assess the number and diversity of marketing-authorized medicines in both countries. The study further examines the differences in NME registration, using databases from the European Medicines Agency (EMA) and the US Food and Drug Administration (FDA). Results: Our study finds that while Kosovo is taking steps to align its pharmaceutical regulations with EU standards, significant gaps remain, particularly in clinical trials, public engagement and digital infrastructure. On the other hand, Croatia exemplifies full EU compliance, with a transparent, efficient, and operational regulatory system that provides better market access, regulatory enforcement, and public interaction. Additionally, the number of marketing-authorized medicines is 26% higher in Croatia compared to Kosovo. One of the most notable findings of this study is the huge contrast between the availability of NMEs in Kosovo and Croatia. The results show that Kosovo has registered only six EMA-approved NMEs and four FDAapproved NMEs between 2021 and 2024. While Croatia counted 33 out of 46 EMA-approved NMEs in 2024 alone. Conclusion: This study presents the first comparative analysis of the pharmaceutical regulatory systems of Croatia and Kosovo, using Croatia as a model for EU-aligned practices. While Croatia has achieved streamlined medicine approvals and broader access through EU integration, Kosovo continues to face implementation challenges. Strengthening digital infrastructure, regulatory enforcement, and EU collaboration are crucial for Kosovo to close the access gap and modernize its system. Croatia’s experience offers valuable guidance for Kosovo’s regulatory development.