Volatile anesthetics are widely known to be immomodulatory, and may have a significant impact on the progression of disease states. Flagellin is a component of Gram negative bacteria and plays a significant role in the pathophysiology of bacterial pneumonia. Here we found that volatile anesthetics, not intravenous anesthetics, significantly attenuated the activation of TLR5 by flagellin and the release of the neutrophil chemoattract IL-8 from lung epithelial cells. Furthermore, flagellin-induced lung injury was significantly attenuated by volatile anesthetics by inhibiting neutrophil migration to bronchoalveolar space. Docking simulations indicated that volatile anesthetics isoflurane and sevoflurane docked into the interphase of TLR5-flagellin binding. Cystic fibrosis (CF) patients are plagued by Pseudomonas aeruginosa pneumonia, which is facilitated by TLR5-flagellin binding. We clinically validated our findings by retrospectively studying the oxygenation in patients with CF under volatile anesthetic-based anesthesia versus intravenous anesthesia showed that former was associated with significantly higher oxygenation compared to intravenous anesthesia, which suggested a protective effect of volatile anesthetics in this patient population.