A nanoimprinting process that enables fabrication of self‐aligned p‐ and n‐type organic thin film transistors with small channel lengths is presented. Nanoimprint lithography with back‐side exposure permit precise definition of the channel length down to the submicrometer regime and a diminutive gate to source/drain overlap. The self‐aligned manufacturing process enables transistor setups with minimized electrode overlaps resulting in distinct decrease of parasitic capacitances and considerable increase in transition frequency. Fully functional small channel OTFTs with p‐ and n‐type semiconductors are fabricated on glass as well as on flexible substrates with transition frequencies up to 400 kHz.