The increasing use of rapidly fluctuating renewable energy sources, such as sunlight, has necessitated the use of supercapacitors, which are a type of energy storage system with high power. Chemically exfoliated graphene oxide (GO) is a representative starting material in the fabrication of supercapacitor electrodes based on reduced GO (rGO). However, the restacking of rGO sheets driven by π–π stacking interactions leads to a significant decrease in the electrochemically active surface area, leading to a loss of energy density. Here, to effectively inhibit restacking and construct a three-dimensional wrinkled structure of rGO (3DWG), we propose an agarose gel-templating method that uses agarose gel as a soft and removable template. The 3DWG, prepared via the sequential steps of gelation, freeze-drying, and calcination, exhibits a macroporous 3D structure and 5.5-fold higher specific capacitance than that of rGO restacked without the agarose template. Further, we demonstrate a “gel-stamping” method to fabricate thin-line patterned 3DWG, which involves the gelation of the GO–agarose gel within micrometer-sized channels of a customized polydimethylsiloxane (PDMS) mold. As an easy and low-cost manufacturing process, the proposed agarose gel templating method could provide a promising strategy for the 3D structuring of rGO.