The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is a global health threat with the potential to cause severe disease manifestations in the lungs. Although clinical descriptions of COVID-19 are currently available, the factors distinguishing SARS-CoV-2 from other respiratory viruses are unknown. Here, we compared the clinical, histopathological, and immunological characteristics of patients with COVID-19 and pandemic influenza A(H1N1). We observed a higher frequency of respiratory symptoms, increased tissue injury markers, a histological pattern of alveolar pneumonia, and higher levels of IL-1RA, TNF-α, CCL3, G-CSF, APRIL, sTNF-R1, sTNF-R2, sCD30, and sCD163 in influenza patients. Conversely, dry cough, gastrointestinal symptoms, interstitial lung pathology, increased Th1 (IL-12, IFN-γ) and Th2 (IL-4, IL-5, IL-10, IL-13) cytokine levels, along with IL-1β, IL-6, CCL11, VEGF, TWEAK, TSLP, MMP-1, and MMP-3, were observed in COVID-19 cases. We demonstrated the diagnostic potential of some clinical and immune factors to differentiate COVID-19 from pandemic influenza A(H1N1). Our data suggest that SARS-CoV-2 induces a dysbalanced polyfunctional inflammatory response that is different from the immune response against influenza. These findings might be relevant for the upcoming 2020-2021 influenza season, which is projected to be historically unique due to its convergence with COVID-19.