We recently reported that a trimeric neck and carbohydrate recognition domain (NCRD) fragment of human surfactant protein D (SP-D), a host defense lectin, with combinatorial substitutions at the 325 and 343 positions (D325A+R343V) exhibits markedly increased antiviral activity for seasonal strains of influenza A virus (IAV). The NCRD binds to glycan rich viral envelope proteins including the hemagglutinin (HA). We now show that replacement of D325 with serine to create D325S+R343V provided equal or, for one viral strain, increased neutralizing activity compared with D325A+R343V. The pandemic H1N1 strains of 1918 and 2009 have only one N-linked glycan site on the head region of the HA and are resistant to inhibition by native SP-D. In contrast, D325A+R343V and D325S+R343V inhibited Cal09 H1N1 and related strains and reduced uptake of Cal09 by epithelial cells. The activity of the double mutants was significantly greater than that of either single mutant (D325A/S or R343V). D325A+R343V and D325S+R343V also strongly inhibited HA activity, and markedly aggregated, the 1968 pandemic H3N2 strain, Aichi68. D325S+R343V significantly reduced viral loads and mortality of mice infected with Aichi68, whereas wild type SP-D NCRD did not. All known human pandemic strains have at least one glycan attachment on the HA head and our results indicate that they may be susceptible to inhibition by modified host defense lectins.