Indonesia has experienced HPAI H5N1 outbreaks since 2003, with its first human case detected in 2005. This study investigates the phylogeography and genetic evolution of highly pathogenic avian influenza (HPAI) H5N1 viruses in Indonesia from 2003 to 2024, revealing significant genetic diversity and reassortment dynamics. Phylogeographic analysis of the haemagglutinin (HA) gene indicates multiple independent viral introductions into Indonesia, with the earliest from Vietnam around 2003–2004 and subsequent incursions from Bangladesh, Timor-Leste, and China. H5N1 viruses demonstrated ongoing evolution, characterised by distinct clades and subclades, particularly clade 2.1, which diversified significantly through reassortment with low-pathogenicity avian influenza strains. The neuraminidase (NA) gene also exhibited substantial genetic diversity, highlighting mutations linked to antiviral resistance. Genomic analyses of internal genes illustrated close genetic ties to contemporary H5N1 strains in Southeast Asia and notable reassortment events. Furthermore, specific amino acid substitutions in viral proteins were identified as being associated with mammalian adaptation and enhanced virulence, notably in the HA and polymerase proteins. These findings underscore the necessity for continuous genomic surveillance to monitor viral evolution and mitigate public health risks associated with potential zoonotic spillover.