Acute respiratory infections (ARI) are the most prevalent illnesses among people of all ages. Influenza viruses, known for frequent genomic changes, require close genetic monitoring to track new strains and evaluate vaccine efficacy. This study aimed to determine the prevalence and variations of seasonal H3N2 influenza among ARI patients at tertiary care hospital in Pondicherry, Southern India, from August 2022 to March 2023 and seasonal trends of H3N2 from 2019 to 2023. We collected 7099 throat swab samples and performed real-time reverse transcription-polymerase chain reaction (RT-PCR) using a magnetic bead-based extraction method. RT-PCR confirmed influenza A and subtype H3N2 presence. Samples with a cyclic threshold (CT) value of ≤ 27 were sequenced. H3N2 peaked from July to November in 2019 and from September to November in 2021. In 2022, peaks shifted to post-November, extending into February-March 2023, with minimal cases in September-October 2022. The study found larger spikes in early 2023, with influenza A being predominant in 13.4% of samples. H3N2 dominated from January to March 2023, while H1N1 was more common earlier. Mutations, both common and novel, were identified. This study highlights the importance of ongoing surveillance and monitoring of H3N2 to guide public health interventions and vaccine development.