Elderberry (Sambucus nigra L.) has traditionally been used for treating influenza and colds. We evaluated the antiviral effect of concentrated juice of elderberry (CJ-E) on the human influenza A virus (IFV). CJ-E had a relatively strong effect on IFV-infected mice, although its anti-IFV activity was weak in a cell culture system. The in vivo anti-IFV activities of the fractions were determined after separating CJ-E by ultrafiltration and anion-exchange chromatography. Oral administration of the high-molecular-weight fractions of CJ-E to IFV-infected mice suppressed viral replication in the bronchoalveolar lavage fluids (BALFs), and increased the level of the IFV-specific neutralizing antibody in the serum, as well as the level of secretory IgA in BALFs and feces. Fr. II from high-molecular-weight fraction HM, which contained acidic polysaccharides, showed relatively strong defense against IFV infection. We conclude that CJ-E had a beneficial effect by the stimulating immune response and preventing viral infection.