Between 14 October 2024 and 24 March 2025, 43 cases of clade 2.3.4.4b highly pathogenic avian influenza (HPAI) type A (H5N1) infections in wild birds and 1 case in a leopard cat were detected through the national HPAI surveillance program. We performed whole-genome sequencing of 51 isolates and investigated their phylogenetic relationships. Phylogenetic analyses identified nine distinct genotypes, designated Kor24–25A to Kor24–25I. The most commonly detected genotype, Kor24–25A (n = 24), was frequently detected in Pelecaniformes and was most prevalent between December 2024 and January 2025. Bayesian continuous and discrete trait phylodynamic analyses using HA gene sequences identified the three most probable routes of viral introduction via Gyeonggi, Jeju, and the southern coastal areas of the Korean Peninsula and suggested that wild ducks served as the primary reservoirs facilitating viral transmission in the wild bird population. During the 2024–2025 season, great egrets (Ardea alba) appeared to be more frequently affected than other wild bird species, suggesting possible seasonal differences in species-specific disease outcomes among wild birds. This study provides valuable insights into the phylodynamics, host associations, and transmission patterns of HPAI H5N1 viruses. It emphasizes the importance of enhanced surveillance programs targeting key avian hosts and high-risk geographic areas.