Introduction: Influenza infection is associated with potential serious complications, increased hospitalization rates, and a higher risk of death. Materials and Methods: A retrospective comparative analysis of selected indicators of hospitalization from the University Hospital in Wroclaw, Poland, was carried out on patients with confirmed influenza infection in comparison to a control group randomly selected from among all other patients hospitalized on the respective wards during the 2018–2019 influenza season. Results: The mean laboratory testing costs for the entire hospital were 3.74-fold higher and the mean imaging test costs were 4.02-fold higher for patients with confirmed influenza than for the control group; the hospital expenses were additionally raised by the cost of antiviral therapy, which is striking when compared against the cost of a single flu vaccine. During the 2018–2019 influenza season, influenza infections among the hospital patients temporarily limited the healthcare service availability in the institution, which resulted in reduced admission rates to the departments related to internal medicine; the mean absence among the hospital staff totaled approximately 7 h per employee, despite 7.3% of the staff having been vaccinated against influenza at the hospital’s expense. Conclusions: There were significant differences in the hospitalization indicators between the patients with confirmed influenza and the control group, which markedly increased the hospital care costs in this multi-specialty university hospital.