The optimization of the performance of optical modulators requires reasonably accurate predictive models for key figures of merit. The interleaved PN junction topology offers the maximum mode/junction overlap and enables the most efficient modulators for depletion-mode operation. Due to the structure of such devices, accurate modeling must be fully three dimensional (3D), representing a nontrivial computational problem. A rigorous 3D model for the modulation efficiency of a silicon-on-insulator interleaved-junction optical phase modulator with submicron dimensions is presented herein. The drift–diffusion and Poisson’s equations are solved on a 3D finite-element mesh, while Maxwell’s equations are solved using the finite-difference time-domain method on 3D Yee cells. The entire modeling process is presented in detail, and all the coefficients required by the model are presented. The model validation suggests < 10% root-mean-square (RMS) error.