A low-cost nanopatterned highly conductive poly(3,4-ethylenedioxy-thiophene) (PEDOT) thin film was fabricated on a flexible plastic substrate via a chemical polymerization method combined with a nanoimprinting technique and used as a platinum (Pt), TCO-free counter electrode for dye-sensitized solar cells (DSSCs). The nanopatterned PEDOT counter electrodes exhibit better functionality as a counter electrode for tri-iodide reduction when compared to nonpatterned PEDOT-based counter electrodes. The Pt and TCO-free DSSCs with a nanopatterned PEDOT-based counter electrode exhibited a power conversion efficiency of 7.1%. The ability to modulate catalytic functionality with changes in nanoscale morphology represents a promising route for developing new counter electrodes of Pt and TCO-free DSSCs.