Influenza seasonality in Singapore shows biannual peaks that coincide with the winters of temperate countries. Human A/H3N2 virus has been circulating in humans for five decades and the virus continues to cause seasonal epidemics worldwide. Antigenic drift is an underlying evolutionary mechanism that accumulates mutations in the viral genomes, allowing the viruses to escape host immune response. In order to understand the current evolution of influenza virus in Singapore, we collected a total of 313 human influenza samples from National University Hospital (NUH) during March 2016–July 2017. Out of these, 82 samples were identified as A/H1N1, 186 as A/H3N2, 44 as influenza B viruses, with one un-determined. Positive A/H3N2 samples were selected for NGS sequencing. Viral RNA was isolated and genome-wide RT-PCR amplification of influenza A viruses was carried out using primers targeting conserved 5’ and 3’ regions. We obtained sufficient NGS coverage for all eight segments of influenza A viruses, and 62 novel A/H3N2 genomes were generated. Gene phylogenies were reconstructed using maximum likelihood method in RAxML v8.0. For the 2016–17 season, A/H3N2 virus was predominant in Singapore, and co-circulated with A/H1N1 and influenza B viruses. Phylogenetic analysis of the HA gene shows that our recent A/H3N2 isolates fall into two clades 3C.2a and 3C.2a1, indicating the Singapore viruses are inter-mingled with global sequences. A/H3N2 virus has drifted significantly in the 2016–17 season, that has led to an update of the WHO influenza virus strain (A/Singapore/INFIMH-16-0019/2016-like) for the 2018 Southern Hemisphere.