In the Energy Finite element Analysis (EFEA) method, the governing differential equations are formulated for an energy variable that has been spatially averaged over a wavelength and time averaged over a period. A finite element approach is used for solving the differential equations numerically. Therefore, a library of elements is necessary for modeling the various wave bearing domains that are present in a structural-acoustic system. Discontinuities between wave bearing domains always exist due to the geometry, from a change in material properties, from multiple components being connected together, or from different media interfacing with each other. Therefore, a library of joints is also necessary for modeling the various types of physical connections which can be encountered in a structural-acoustic system.In this paper, a new joint formulation is presented for using incompatible meshes in EFEA models, when shapes and/or sizes of elements at structural-acoustic interfaces do not match. The algorithm which identifies automatically the joints in a finite element model is presented, and the implementation of the joints in the EFEA solver is discussed. The new developments are tested by comparing results generated using incompatible models for a simple configuration, and through comparison to test data for a representative automotive air-borne noise application.