Highly pathogenic avian influenza A(H5N1) hemagglutinin (HA) clade 2.3.4.4b viruses are now circulating in wild birds and agricultural species (poultry and dairy cows), resulting in multiple human infections. Both preclinical and clinical data for treating A(H5N1) with US Food and Drug Administration–approved anti-influenza drugs are limited. Here, we examined the protection conferred by one, two, or three doses of the newest approved anti-influenza drug, baloxavir, in ferrets lethally challenged with either an avian- or bovine-origin A(H5N1) virus. All dosing regimens improved survival and clinical outcomes with protection ranging from 50 to 100%. Compared with vehicle-only treatment, baloxavir regimens decreased virus shedding, lung pathology, and viremia and eliminated viral spread to the brain. Multidose therapy yielded the best outcomes overall. Single-dose baloxavir prophylaxis with an avian virus challenge resulted in the low-frequency presence of polymerase acidic (PA) protein containing the E23K substitution, whereas all treatment regimens after a bovine-origin virus challenge induced at least one instance of PA containing the I38T substitution. Both PA-E23K and PA-I38T were predicted to decrease potential baloxavir–PA protein interactions, and they phenotypically reduced susceptibility of the virus to baloxavir by 3.8-fold [50% effective concentration (EC50) = 15.13 nanomolar, PA-E23K] and 77.3-fold (EC50 = 307.40 nanomolar, PA-I38T) in polymerase assays. Baloxavir is a single-dose drug for treating seasonal influenza. We show that multidose regimens of baloxavir may be most efficacious against highly pathogenic avian influenza A(H5N1) in a preclinical ferret model, with effective control of both severe disease and neurological involvement.