Brain metastasis (BM) is associated with poor prognosis, recurrence, and death in patients with non-small cell lung cancer (NSCLC). Therefore, a better understanding of molecular mechanisms underlying NSCLC development and progression could provide helpful insights for NSCLC prevention and effective treatment. Melanophilin (MLPH), an actin-based transport binding partner, involves in cancer progression. However, the role of MLPH in NSCLC remains unclear. Here we elucidated the functional significance, molecular mechanisms and clinical impact of MLPH in NSCLC. RNA-Sequencing was performed to identify differentially expressed genes in lung tissues of NSCLC patients with (BM+) and without BM (BM-). The expression of MLPH was examined in the serum of BM+ and BM- patients by PCR. Integrative database analysis was used to examine MLPH levels in NSCLC tissues and analyze the relationship between MLPH levels and patient survival. Lentivirus containing small hairpin (sh) RNA targeting MLPH or empty vector was designed to explore its role in NSCLC. The cell counting kit-8 assay, wound healing assay, transwell assay, flow cytometry analysis, Phalloidin staining, xenografted tumor model and brain metastasis model were used to determine the effects of MLPH on the proliferation, migration, invasion, EMT, tumorigenesis and brain metastasis of NSCLC. Western blot analysis was used to explore the underlying mechanism. High-throughput sequencing showed that MLPH mRNA was significantly differentially expressed in lung tumors between BM+ and BM- NSCLC patients. MLPH was frequently overexpressed in NSCLC tissues and cells, and high levels of MLPH correlated with poor prognosis of NSCLC patients. Silencing MLPH by shRNA suppressed NSCLC cell proliferation, migration, invasion and TGF-β-induced EMT, and triggered cell cycle arrest and apoptosis. Being in consistent with the in vitro findings, the in vivo experiment exhibited that knockdown of MLPH inhibited xenograft tumorigenesis and brain metastasis in nude mice. Mechanically, we identified TGF-β as a key downstream effector of MLPH. MLPH silencing attenuated Cdc42/PAK1 signaling activation at least in part through the downregulation of TGF-β. Furthermore, EMT phenotypes changes caused by MLPH knockdown were partially dependent on TGF-β inhibition. Our findings uncovered the role of MLPH in NSCLC progression and provided evidence for MLPH positively modulating the Cdc42/PAK1 signaling pathway to promote EMT and metastasis via TGF-β in NSCLC cells. MLPH may have the potential as a therapeutic target against metastatic NSCLC.