We herein report the pulmonary histopathological findings of an autopsy case of post-pandemic season A/H1N1pdm09 infection-associated acute respiratory distress syndrome (ARDS). The lung histology predominantly exhibited findings indicative of the exudative phase of diffuse alveolar damage, with similar inflammation severity observed in all sections. Furthermore, the lung sections only showed a few A/H1N1pdm09 antigen-positive cells along with a low viral RNA copy number. The sequence of the viral hemagglutinin receptor binding site identified a preference for α-2,6 linked sialic acid, suggesting low alveolar epithelial cell infectivity. The pathological findings, in this case, differed in several aspects from those of the first autopsy case of A/H1N1pdm09 infection-associated ARDS in Japan, reported during the 2009 pandemic season. In conclusion, pathological and molecular biological examinations suggested that in the post-pandemic season A/H1N1pdm09 infection, the infection-associated ARDS was not caused by direct infection-induced damage to the alveolar epithelial cells but was rather a result of indirect sepsis-mediated endothelial cell damage.