Cell-penetrating peptides (CPPs) have shown promise in non-permeable therapeutic drug delivery, owing to their ability to transport a variety of cargo molecules across the cell membranes and their non-cytotoxicity. Drosophila antennapedia homeodomain-derived CPP-Penetratin (RQIKIWFQNRRMKWKK), being rich in positively charged residues, has been increasingly used as a potential drug carrier for the treatment of various purposes. Penetratin can breach the tight endothelial network, blood-brain-barrier (BBB), enabling treatment of several neurodegenerative maladies including Alzheimer's disease, Parkinson's disease, and Huntington's disease. However, detailed structural knowledge and the mechanism of Penetratin action remains unknown. This study defines structural features of the Penetratin derived peptide – DK17 (DRQIKIWFQNRRMKWKK) in several model membranes and describes a membrane-induced conformational transition of the DK17 peptide in these environments. A series of biophysical experiments, including high-resolution NMR spectroscopy, provides the three-dimensional structure of DK17 in different membranes mimicking the BBB or total brain lipid extract. MD simulations support the experimental results showing preferential binding of DK17 to particular lipids at atomic resolution. The peptide conserves the structure of the subdomain spanning residues Ile6-Arg11, despite considerable conformational variation to different membrane models. In vivo data suggest that the wild-type, not a mutated sequence, enters the central nervous system. Together, these data highlight important structural and functional attributes of DK17 that could be utilized in drug delivery for neurodegenerative disorders.