We investigated the molecular interactions of a cell penetrating peptide (CPP) Pep-1 with model cell membranes using sum frequency generation (SFG) vibrational spectroscopy, supplemented by attenuated total reflectance - Fourier transform infrared spectroscopy (ATR-FTIR). Hydrogenated and deuterated 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG and dDPPG) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (POPG), were used in the experiments to represent gel-phase and fluid-phase lipid bilayers, respectively. Our SFG results indicated that Pep-1 molecules adopted a β-sheet conformation when adsorbed to the surface of gel-phase DPPG lipid bilayers. When interacting with fluid-phase POPG lipid bilayers, Pep-1 adopted a mix of α-helical and β-sheet structures over a broad range of peptide concentrations. The orientation distribution of the α-helical Pep-1 segment associated with the fluid-phase bilayers was found to depend on the peptide concentration. SFG orientation analysis showed that Pep-1 molecules adopted an orientation nearly perpendicular to the plane of the bilayer for peptide concentrations of 0.28 μM and 1.4 μM. When the Pep-1 concentration was increased to 7.0 μM, combined SFG and ATR-FTIR measurements showed that Pep-1 molecules were associated with the bilayer with a broad orientation distribution. Our results demonstrated that lipid bilayer phase and peptide concentration affect the conformation and orientation of Pep-1 molecules associated with model cell membranes, which is crucial to the translocation process of CPPs. A combination of SFG and ATR-FTIR studies can be used to determine the conformation and orientation of CPPs interacting with model cell membranes in situ.