H9N2 avian influenza virus has been continuously circulating among poultry and could infect mammals, indicating that this virus is a potential pandemic strain. During influenza pandemics, secondary bacterial (particularly pneumococcal) pneumonia usually contributes to excess mortality. In the present study, we observed the dynamic effect of H9N2 virus infection on host defense against secondary pneumococcal infection in mice. BALB/c mice were intranasally inoculated with 1.2 × 105 plaque forming units (PFU) of H9N2 virus followed by 1 × 106 colony forming units of Streptococcus pneumoniae on 7, 14 or 28 days post-H9N2 infection (D.P.I.). The bacterial load, histopathology, body weight and survival were assessed after pneumococcal infection. Our results showed that H9N2 virus infection had no significant impact on host resistance to secondary pneumococcal infection on 7 D.P.I. However, H9N2 virus infection increased pulmonary pneumococcal clearance and reduced pneumococcal pneumonia-induced morbidity after secondary pneumococcal infection on 14 or 28 D.P.I., as reflected by significantly decreased bacterial loads, markedly alleviated pulmonary histopathological changes and significantly reduced weight loss in mice infected with H9N2 virus followed by S. pneumoniae compared with mice infected only with S. pneumoniae. Further, the significantly decreased bacterial loads were observed when mice were previously infected with a higher dose (1.2 × 106 PFU) of H9N2 virus. Besides, similar to the results obtained in BALB/c mice, improvement in pulmonary pneumococcal clearance was also observed in C57BL/6 mice. Overall, our results showed that pulmonary pneumococcal clearance is improved after resolution of H9N2 virus infection in mice.