A method for the sustained delivery of exenatide was proposed using nanoparticles (NPs) with a core/shell structure. The interactions between lipid bilayers and Pluronics were utilized to form various NPs using a layer-by-layer approach. Transmittance electron microscopy and dynamic light scattering were used to examine the morphology of the NPs. The in vitro release pattern was observed as a function of changes in the structure of the NPs, and the structural integrity of exenatide released was examined by SDS–PAGE analysis. Pharmacokinetics and antidiabetic effects were also observed with the structural change of NPs using in vivo animal models. In vitro–in vivo correlation was discussed in relation to manipulation of the NP structures.