Neurodevelopmental disorders (NDDs) are characterized by diverse genetic underpinnings and abnormalities in the structure and function of the central nervous system. While the lung-specific SFTPC gene is critical for pulmonary development and homeostasis, its potential involvement in NDDs has not been previously explored. In this study, we identified compound heterozygous variants of SFTPC in two children diagnosed with NDDs, inherited from carrier parents. Bioinformatic analyses predicted these variants to be deleterious, and patient blood samples confirmed reduced SFTPC protein levels. To investigate the functional impact of these mutations, we generated a Sftpc-knock-in (Sftpc-KI) mouse model carrying the defective alleles. The Sftpc-KI mice exhibited significantly reduced Sftpc expression in both lung and blood samples. Remarkably, despite its lung-specific expression, Sftpc-KI mice displayed pronounced impairments in neurobehavioral performance. Proteomic analyses of the Sftpc-KI mouse brain revealed dysregulated proteins associated with neuroinflammation. Furthermore, primary microglial cells isolated from these mice exhibited heightened expression of M1 activation markers, indicating aberrant microglial activation. Our findings uncover a previously unrecognized connection between lung-specific SFTPC dysfunction and neurodevelopmental disorders, suggesting the existence of a novel brain-lung axis and opening new avenues for research into the molecular mechanisms underlying NDDs.