This article utilizes a topology optimization approach to design planar multilayer transitions between substrate integrated waveguides (SIWs) and rectangular waveguides (RWGs). The optimization problem is formulated based on the modal field analyses and Maxwell's equations in the time domain solved by the finite-difference time-domain (FDTD) method. We present a time-domain boundary condition based on the Klein–Gordon equation to split traveling waves at homogeneous waveguide ports. We employ the boundary condition to compute portal quantities and to devise an adjoint-field system that enabled an efficient computation of the objective function gradient. We solve design problems that include more than 105 000 design variables by using less than 400 solutions of Maxwell's equations. Moreover, a new formulation that effectively combats the development of in-band resonances in the design is presented. The transition configuration allows the direct mount of conventional RWG sections on the circuit board and aims to cover the entire K-band. The guiding structure of the optimized transition requires blind vias, which is realized by a simple and cost-efficient technique. In addition, the transition is optimized for three different setups that can be used to provide different field polarizations. The proposed transitions show less than 1-dB insertion loss and around 15-dB return loss over the frequency interval 18–28 GHz. Several prototypes are fabricated with an excellent match between the simulation and measurement results.