Some probiotics possess immunomodulatory activities and have been used as complementary and alternative medicines. We previously found that 10 lactic acid bacteria (LAB) strains isolated from traditional Mongolian dairy products showed probiotic potential in vitro. In this study, we assessed the immunomodulatory activity of 10 LABs on influenza virus (IFV) infection in relation to their efficacies in IFV-infected mice. In an intranasal IFV infection model in mice, oral administration of boiled Lactobacillus plantarum 06CC2 strain (20 mg/mouse), one of the 10 LABs, twice daily for 10 days starting two days before infection was significantly effective in protecting the body weight loss of infected mice, reducing virus yields in the lungs on days 2, 4, and 6 after infection, and prolonging survival times without toxicity. The total numbers of infiltrated cells in the bronchoalveolar lavage fluid (BALF), especially macrophages and neutrophils, were significantly reduced by 06CC2 administration on day 2. On day 2, tumor necrosis factor (TNF)-α production in BALF was also reduced significantly, but interferon-α, interleukin-12, and interferon-γ productions were augmented and natural killer (NK) cell activity was significantly elevated. Furthermore, the gene expressions of interleukin-12 receptor and interferon-γ in Peyer's patches were augmented by 06CC2 administration on day 2. Thus, 06CC2 was suggested to alleviate influenza symptoms in mice in correlation with the augmentation of NK cell activity associated with the enhancement of interferon-α and Th1 cytokine productions through intestinal immunity and the reduction of TNF-α in the early stage of infection.