The Energy Finite Element Analysis (EFEA) has been utilized successfully for modeling complex structural-acoustic systems with isotropic structural material properties. In this paper, a formulation for modeling structures made out of composite materials is presented. An approach based on spectral finite element analysis is utilized first for developing the equivalent material properties for the composite material. These equivalent properties are employed in the EFEA governing differential equations for representing the composite materials and deriving the element level matrices. The power transmission characteristics at connections between members made out of non-isotropic composite material are considered for deriving suitable power transmission coefficients at junctions of interconnected members. These coefficients are utilized for computing the joint matrix that is needed to assemble the global system of EFEA equations. The global system of EFEA equations is solved numerically and the vibration levels within the entire system can be computed. The new EFEA formulation for modeling composite laminate structures is validated through comparison to test data collected from a representative composite aircraft fuselage that is made out of a composite outer shell and composite frames and stiffeners. NASA Langley constructed the composite cylinder and conducted the test measurements utilized in this work.