Background Influenza is difficult to distinguish clinically from other acute respiratory infections. Rapid laboratory diagnosis can help initiate early effective antiviral treatment and isolation. Aim Implementing a novel point-of-care test (POCT) for influenza in the emergency department (ED) could improve treatment and isolation strategies and reduce the length-of-stay (LOS). Methods In a prospective, controlled observational cohort study, we enrolled patients admitted due to acute respiratory illness to two public hospitals in Bergen, Norway, one using a rapid POCT for influenza (n=400), the other (n=167) using conventional rapid lab-based assay. Results The prevalence of influenza was similar in the two hospitals (154/400, 38% versus 38%, 63/167, p=0.863), and most patients in both hospitals received antiviral (83% versus 81%,p=0.703) and antibiotic treatment (76% versus 73%, p= 0.469). Isolation was more often initiated in the ED in the hospital using POCT (91% versus 80%, p=0.025). Diagnosis by POCT was associated with shorter hospital stay, while old age, diabetes, cancer, use of antibiotics, particularly broad-spectrum antibiotics, were associated with prolonged stay. Conclusions POCT implementation in the ED resulted in improved targeted isolation and shorter LOS. Regardless of POCT-use, most influenza patients received antivirals (>80%) and antibiotics (>70%).