Electro-optic (EO) polymers are promising candidates for active materials especially for realizing the optical modulator devices. They offer high bit rate operations and low driving voltage. We study a thermally-curable polycyanurate (PCN) doped with a high nonlinear optical chromophore to create a new type of guest–host EO polymer with thermally stable second-order nonlinearity. We fabricated the PCN-based EO polymer optical waveguide by implementing simple thermal imprint lithography technology using a poly(dimethylsiloxane) (PDMS) mold. We fine-tuned the refractive index of core and claddings materials by optimizing the chromophore concentration of the core and by changing the fluoride content of the claddings. We realized a single-mode propagation of optical waveguide at 1300 nm.