Invasive group A streptococcal disease which is caused by the bacterial pathogen Streptococcus pyogenes disproportionately affects disadvantaged communities including Aboriginal and Torres Strait Islander Australians. To better define the temporal dynamics of invasive S. pyogenes, we examined the population genomics of clinical cases between the hyperendemic Top End of the Northern Territory and lower incidence regions in temperate south-east (SE) of Australia between January 2011 to February 2023. Population genomics revealed that the Top End was characterised by waves of lineage replacement compared to endemic maintenance in the SE. Despite distinct circulating lineages, the frequency of genes in the bacterial population was maintained across geographical and temporal periods. A multi-strain transmission model was applied to this dataset which revealed that transmission rate, population size, and human movement, are key parameters in replicating the observed lineage dynamics. These findings provide a baseline for defining the national genomic epidemiology of invasive S. pyogenes and suggest that interventions such as vaccines-in-development without broad cross-protection could also lead to lineage replacement.