Zanamivir has been shown to inhibit both human and avian influenza viral neuraminidases (NAs) and has been approved in several countries for the treatment and prophylaxis of influenza infection. Reliable monitoring of drug resistance is important for assessment of the impact of drug therapy on circulating virus populations. This study compares the current fluorometric (FL) method for evaluating zanamivir susceptibility with a recently developed chemiluminescent (CL) NA activity assay using viruses representative of all nine NA subtypes. The CL assay displayed signal/noise ratios that are 50–100 times greater than those associated with the FL assay. Human H3N2 strains appeared to exhibit greater NA activity relative to avian subtypes with the FL substrate but not with the CL substrate. Additionally, the CL assay remained linear over three orders of magnitude compared to only one order of magnitude for the FL assay. Four of the nine NA subtypes tested in this study displayed slightly higher inhibitor concentration that inhibits 50% of neuraminidase activity values by CL than by FL, while four displayed the opposite effect. Implications for the routine determination of resistance to NA inhibitors are discussed.