Background: Respiratory tract infections were associated with acute exacerbations of heart failure (HF). However, the role of the influenza virus, a major agent of such infections, in this population remained unclear. Method: During the influenza virus seasons of 2013 and 2014 we prospectively assessed influenza respiratory illnesses in a cohort of adults primarily hospitalized for management of acute decompensated HF and a cohort of HF outpatients. Qualitative RT-PCR for influenza A (A/H1, A/H12009pdm, A/H3) and B virus testing was performed on nasopharyngeal swab samples. Result: A total of 121 patients were included, 58.3% males (n = 70), mean age 57.7 years old (±14.0), mean left ejection fraction 35.3 (±9.8). Of these, 50.4% were inpatients (n = 61). The prevalence of symptoms of respiratory infections was 28.0% (n = 34) and 4.9% (n = 6) of all samples were positive for influenza virus. Only influenza A was detected and all cases were among inpatients. Influenza-positive patients had a greater need for antimicrobials (83.3%, n = 5; 16.3%, n = 9; p = 0.001) and for mechanical ventilation (50.0%, n = 3; 3.6%, n = 2; p < 0.001) than Influenza-negative patients. The prevalence of influenza virus was not related to mortality (OR 4.58; p = 0.16). Conclusion: Although not common, the influenza virus infection resulted in worst outcomes, with a greater need for antimicrobials and mechanical ventilation. Immunization and antiviral treatment in high risk patients may positively impact their outcomes.