The design of microwave circuits requires detailed knowledge on the electromagnetic properties of the transmission lines used. This can be obtained by applying Maxwell’s equations to a longitudinally homogeneous waveguide structure, which results in an eigenvalue problem for the propagation constant. Special attention is paid to the so‐called perfectly matched layer boundary conditions (PML). Using the finite integration technique we get an algebraic formulation. The finite volume of the PML introduces additional modes that are not an intrinsic property of the waveguide. In the presence of losses or absorbing boundary conditions the matrix of the eigenvalue problem is complex. A method which avoids the computation of all eigenvalues is presented in an effort to find the few propagating modes one is interested in. This method is an extension of a solver presented by the authors in a previous paper which analyses the lossless case. Using mapping relations between the planes of eigenvalues and propagation constants a strip in the complex plane is determined containing the desired propagation constants and some that correspond to the PML modes. In an additional step the PML modes are eliminated.The numerical effort of the presented method is reduced considerably compared to a full calculation of all eigenvalues.