To elucidate the effect of fowl adenovirus (FAdV)-C in specific-pathogen-free (SPF) chickens, we investigated the pathogenicity, body weights, enzymatic systems, and immune organs of chickens in response to Newcastle disease virus (NDV) and avian influenza virus subtype H9 (AIV-H9) vaccination. Chickens were divided randomly into four groups, which included injection groups (FAdV-C, vaccination, and FAdV-C plus vaccination) and a negative control group. The results indicated that FAdV-C was highly pathogenic in SPF chickens and led to a 40% mortality rate and growth retardation, compared with the control birds. Significant changes in clinical chemical markers of all infected birds, together with histopathological lesions, indicated impairment of the liver and heart integrity and function. Furthermore, chickens in the FAdV-C plus vaccination group had significantly lower titers of antibodies against NDV and AIV-H9 than the uninfected and vaccinated chickens. The results of this study provide new insights into the pathogenesis of hydropericardium syndrome, a disease that progresses to a metabolic disorder and causes serious growth retardation and immunosuppression.