A rigorous and efficient method for characterizing E-/H-plane multiport junctions in rectangular waveguides is presented by using the mode-matching method combined with Fourier transform technique. The method is based on a field-theoretical full-wave approach. The electric and magnetic fields of a main waveguide in the junction are expressed in terms of Fourier integrals and matched in the Fourier transformed domain to the aperture fields expanded by the normal modes in each of arm waveguides. This yields a set of linear equations in analytically closed form to calculate the scattering parameters of the multiport systems. The numerical examples for a Magic-T junction and an asymmetric E-/H-plane three-port junction verify the accuracy and usefulness of the present method.