A common method of solving initial boundary value problems is separation of variables, denoted as modal analysis in the field of flexible structures. For systems with undamped boundary conditions the method is well-established, but for systems with boundary damping it does not provide closed form solutions. In this paper the exact modal series solution for second order systems with damped boundaries is derived with explicit expressions for the series coefficients. Knowledge of these coefficients enables practical applications of the solution, such as finite dimension approximation. The key element of the derivation is a new orthogonality condition for the damped eigenfunctions. The modal series is also transformed into a traveling wave form. The solution, which is the extension of the classical D’Alembert formula, is represented by a single equivalent propagating wave. A component of the solution, denoted by “end waves”, is identified to provide the continuity of the systems displacement response.