Rapid point-of-care (POC) detection of influenza A virus is critical for timely and effective flu prevention and control. In this study, we developed a hybridization chain reaction (HCR)-based assay, through coupling HCR reaction with fluorescence quenching by graphene oxide (GO), for the rapid detection of influenza A virus. The target is detected as it triggers HCR, which results in the extension of short DNA chains, protecting the 6-carboxy-fluorescein amidite (FAM) group from GO quenching. The results demonstrate that it could specifically recognize target nucleic acid fragment of influenza A virus from other pathogen, and even from single-base mismatched oligonucleotides. A good linear correlation between fluorescence intensity and the target concentrations ranging from 10 to 40 nmol/L was achieved, with a detection limit of 5 nmol/L. Its detection performance was verified on nasopharyngeal swab samples, which is the first clinical application of HCR-based influenza assay. This HCR-based method shows many advantages including the enzyme-free amplification of nucleic acids, simple reaction system and convenient protocols, suggesting its availability for POC detection.