In this paper, we develop a computer-aided design (CAD) tool for physical design of optoelectronic system-on-a-package (SOP) using optical waveguide interconnects. The tool assigns the optimal location to modules and replaces long electrical interconnects with optical waveguide interconnects in order to maximize the overall performance of the optoelectronic system-on-a-package. More than 47% improvement in system-on-a-package performance is obtained through the use of optical waveguide interconnects.