Acute respiratory distress syndrome constitutes a significant disease burden with regard to both morbidity and mortality. Current therapies are mostly supportive and do not address the underlying pathophysiologic mechanisms. Removal of protein-rich alveolar edema—a clinical hallmark of acute respiratory distress syndrome—is critical for survival. Here, we describe a transforming growth factor (TGF)-β-triggered mechanism, in which megalin, the primary mediator of alveolar protein transport, is negatively regulated by glycogen synthase kinase (GSK) 3β, with protein phosphatase 1 and nuclear inhibitor of protein phosphatase 1 being involved in the signaling cascade. Inhibition of GSK3β rescued transepithelial protein clearance in primary alveolar epithelial cells after TGF-β treatment. Moreover, in a bleomycin-based model of acute lung injury, megalin+/- animals (the megalin-/- variant is lethal due to postnatal respiratory failure) showed a marked increase in intra-alveolar protein and more severe lung injury compared with wild-type littermates. In contrast, wild-type mice treated with the clinically relevant GSK3β inhibitors, tideglusib and valproate, exhibited significantly decreased alveolar protein concentrations, which was associated with improved lung function and histopathology. Together, we discovered that the TGF-β-GSK3β-megalin axis is centrally involved in disturbances of alveolar protein clearance in acute lung injury and provide preclinical evidence for therapeutic efficacy of GSK3β inhibition.