Mycoplasma synoviae (MS) is an important pathogen of domestic poultry and is prevalent in commercial layers. Avian influenza (AI; H9N2) infections are emerging respiratory problems causing huge economic losses to the poultry industry, especially in the presence of other co-infecting pathogens. The possible role of MS vaccination and response to AI (H9N2) virus in commercial layers was evaluated during this study. Experimental commercial layers were divided into different groups which were identified as follows: non-vaccinated non-challenged (NVNC), non-vaccinated challenged (NVC), vaccinated non-challenged (VNC), and vaccinated challenged (VC). The titer of AI antibodies was measured pre- and post-challenge to confirm experimental infection. Infected layers showed clinical signs of differing severity, with the most prominent disease signs and mortality (25%) appearing in layers of the VC group. Moreover, the layers in VC group showed a significant decrease in weight and enhanced gross lesions. All infected layers showed positive results for virus shedding; however, the pattern of virus shedding was different, with layers of VC group showing more pronounced virus excretion than the layers in the NVC group. In addition, layers of VC group showed significantly reduced antibody responses and interferon gene expression when compared with the layers of NVC group. The present study revealed that MS vaccine could facilitate replication of avian influenza viruses and thus avian influenza virus infections can be worse after MS vaccination, especially in AIV-endemic areas.