When administered prophylactically, we show that the Toll‐like receptor‐2 (TLR‐2) agonist PEG‐Pam₂Cys (pegylated‐S‐(2,3‐bis(palmitoyloxy)propyl)cysteine) not only mediates potent anti‐viral activity against influenza virus but also reduces the impact of secondary infections with Streptococcus pneumoniae (the pneumococcus) by reducing (i) pulmonary viral and bacterial burdens, (ii) the levels of proinflammatory cytokines that normally accompany influenza and S. pneumoniae secondary infections and (iii) the vascular permeability of the pulmonary tract that can allow bacterial invasion of the blood in mice. We also show that an inactivated detergent‐disrupted influenza virus vaccine formulated with the Pam₂Cys‐based adjuvant R₄‐Pam₂Cys provides the host with both immediate and long‐term protection against secondary pneumococcal infections following influenza virus infection through innate and specific immune mechanisms, respectively. Vaccinated animals generated influenza virus‐specific immune responses that provided the host with long‐term protection against influenza virus and its sequelae. This vaccine, which generates an immediate response, provides an additional countermeasure, which is ideal for use even in the midst of an influenza outbreak.