Highly pathogenic avian influenza (HPAI) H5N1 continues to pose a major threat to animal and public health. Since its emergence, clade 2.3.4.4b has become the dominant global lineage, associated with widespread outbreaks in Europe. This study aimed to characterise the H5N1 strains detected in backyard chickens in Serbia and investigate their phylogenetic and phylogeographic relationships with historical and currently circulating strains in Serbia and the broader region. Samples collected in 2024 were tested by qRT-PCR, and positive samples were propagated in MDCK cells. Whole genome sequencing of isolated virus was performed using the MinION Mk1C platform (ONT, Oxford, UK). Bayesian phylogenetic and phylogeographic analyses were conducted using BEAST X and SPREAD3 v.9.6. The results revealed three independent introductions of H5N1 into Serbia between 2020 and 2024. The spatiotemporal diffusion patterns confirmed both north–south and west–east viral spread from Northern and Central Europe into the Balkans. Additionally, Serbia was identified as a critical transit and divergence point in the regional transmission network, highlighting its role in the spread of H5N1 between Western and Eastern Europe. These findings underscore the importance of continued genomic surveillance in both domestic and wild bird populations to better understand and reduce HPAI spread.