The COVID-19 pandemic highlighted the need for rapid and accurate diagnosis of respiratory viral infections and reinforced the importance of integrated respiratory virus surveillance systems. Rapid diagnostic tests (RDTs) provide timely results but may show limited sensitivity compared with molecular assays. This study aimed to evaluate the diagnostic performance of the BD Veritor™ System for Rapid Detection of Respiratory Viruses for detecting respiratory syncytial virus (RSV), Influenza A, and Influenza B in Mali, using multiplex real-time RT-PCR as the reference standard. A total of 1202 nasopharyngeal and/or oropharyngeal swab specimens collected between March 2020 and March 2022 from suspected respiratory infection cases were analyzed. Samples were tested using the BD Veritor™ rapid antigen assay and compared with the ViroQ^® SARS-CoV-2/FluA/FluB/RSV multiplex RT-PCR assay performed on the LightCycler^® 480 II system. Diagnostic performance was assessed using sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and Cohen’s kappa coefficient. The BD Veritor™ assay demonstrated consistently high specificity (>91%) for all viral targets, whereas sensitivity remained low, ranging from 21.05% to 30.43%. Positive predictive values ranged from 24.78% to 46.15%, while negative predictive values remained above 83%. Agreement with RT-PCR was low (κ = 0.14–0.24), indicating limited concordance between the two methods. The reduced sensitivity observed may partly be explained by low viral loads, prolonged frozen storage of samples before antigen testing, and the complex epidemiological context associated with the co-circulation of respiratory viruses during the COVID-19 pandemic. Although the BD Veritor™ assay may provide useful support for rapid clinical orientation and triage in resource-limited settings, negative results should be interpreted cautiously and confirmed by RT-PCR whenever possible.