This study proposes a simple and cost-effective method of fabricating a double-layer polymeric optical waveguide, using two hot-embossing processes with a single stamp and template for passive alignment between the top and bottom layers. The two hot-embossing processes were conducted sequentially on the top layer and the bottom layer of the polymer layer. The second hot-embossing process was conducted after fabricating the buffer layer on the surface of the polymeric channel structure to control deformation and destruction of the previously fabricated polymeric channel structure. Passive alignment of the channel structure for the top layer and the bottom layer was automatically performed by simple insertion of the stamp and polymer layer using a metal template with the same dimensions (width x length) as the stamp. Regarding the polymer layer, the buffer layer on the side with the channel structure was coated, whereas the layer contacting the stamp did not have a buffer layer. For the purposes of this study, a 2 x 50 channel polymeric multimode optical waveguide was fabricated using a stamp with 50 straight ribs, without any coupling between the layers. The fabricated optical waveguide was controlled within positional tolerances of less than ± 5 μm between layers; propagation loss of below 0.2 dB/cm at 850 nm; and channel uniformity of below 0.5 dB.