Understanding the diversity and circulation dynamics of seasonal influenza viruses is key to public health decision-making. The limited genetic information of pre-pandemic seasonal IAVs in Chile has made it difficult to accurately reconstruct the phylogenetic relationships of these viruses within the country. The objective of this study was to determine the genetic diversity and estimate the antigenic evolution of pre-pandemic human seasonal IAVs in Chile. We sequenced the complete genome of 42 historic IAV obtained between 1996 to 2007. The phylogeny was determined using HA sequences and complemented using other segments. Time-scale phylogenetic analyses revealed that diversity of pre-pandemic human seasonal IAVs in Chile have been influenced by continuous introductions of new A/H1N1 and A/H3N2 lineages and constant viral exchange between Chile and the rest of the countries every year. Besides, wide genetic and antigenic diversity was observed co-circulating in some years and introduced lineages every year become extinct at the end of each season. These results provide important knowledge about genetic diversity and evolutionary patterns of pre-pandemic human seasonal IAVs in Chile, which can help to design optimal surveillance systems and prevention strategies in the country, however, future studies with current sequences should be conducted.