High pathogenicity avian influenza virus impacts poultry and wild birds worldwide. Since the introduction of clade 2.3.4.4b H5N1 isolates in Japan in late 2021, new cases have been reported in domestic birds and poultry each winter. To understand the role of wild birds in introducing these viruses in Japan, a phylodynamic analysis based on geography and host species was conducted using H5N1 isolates in Japan from 2021–2025. A total of 892 hemagglutinin gene sequences of H5N1 viruses, collected from birds between June 2021 and May 2025, along with additional sequences that were highly similar to those of Japanese isolates, were obtained from a public database. The role of wild birds in the transmission dynamics of H5N1 isolates in Japan across four winter seasons (2021–2025) was assessed using a Bayesian phylodynamic approach with a Multi-Type Birth-Death model. Phylodynamic analysis revealed that the clade 2.3.4.4b comprised three distinct subgroups, G2b, G2c, and G2d, which were prevalent during the winter seasons. Isolates from G2b and G2c were linked to common ancestral strains from North Asia and Northeast Asia, respectively. Meanwhile, G2d, the dominant strain in Japan from 2021 to 2025, shared an ancestral strain from the Northwest America. During the winters of 2023–2025, the ancestral strain was traced back to Northeast Asia, indicating a shift in the viral origin. This transition suggests an increase in virus migration events and expansion of host diversity, implying that Japan may function as a hub for intercontinental virus introductions, receiving multiple independent viral entries from North Asia, Northeast Asia, and Northwest America. Additionally, waterfowl and raptors played a role in introducing viruses into Japan, while poultry and crows generally serving as dead-end hosts. However, the continuous introduction of H5N1 isolates into Japan each winter can alter the disease transmission pattern observed in crows, resulting in more virus spillover from crows to other hosts, such as poultry and charadriiformes. These findings emphasize the importance of continuous monitoring and prompt information sharing to understand the global dynamics of viruses better.