This paper presents an analysis methodology for composite sandwich panel 90° closeout with multi-layered non-uniform facesheets and core. A detailed 2D finite element model was constructed to model honeycomb core through the thickness as well as simulate top and bottom facesheets and the transition region. 2D equivalent material properties of the facesheets are calculated based on classical lamination theory. Elemental stresses of core are used to calculate failure index and margin of safety for various loading conditions based on tension/compression and shear interaction theory. Facesheet strength is checked by interlaminar shear and tension interaction equation with the utilization of failure index. Theoretical failure modes and critical locations obtained from this approach are compared with structural testing of specimens. The predicted failure loads, deflection, facesheet load ratio, and strains are in good agreement with test data. The methodology is verified to be a simple, efficient, and reliable method for the analysis of composite sandwich closeout structures.