A rigorous synthesis rule of corrugated waveguide filters is developed, employing the Gel``sfand-Levitan-Marchenko inverse scattering method, when the reflection coefficient is a rational function. The inverse scattering problem for the two-component coupled wave equation (so-called Zakharov-Shabat equation), a particular form of which is the basic equation for a corrugated waveguide, is applied to reconstruct the coupling coefficient. In the course of developing the synthesis method, the Gel``sfand-Levitan-Marchenko integral equation for the Zakharov-Shabat equation is shown to be reducible to a matrix equation amenable to simple numerical calculation, when the reflection coefficient is a rational function.