In this paper, a simple and facile method to fabricate micro‐ and nanopatterned Nafion thin films with tunable mechanical and electrical properties is reported. To achieve this, a novel thermal evaporation‐induced capillary force lithography method with a swelling process to obtain enhanced pattern fidelity in micro‐ and nanomolded Nafion films is combined. It is demonstrated that structural fidelity and mechanical properties of micro‐ and nanopatterned Nafion thin films can be modulated by changing fabrication parameters, such as swelling time, Nafion polymer concentration, and curing temperature. Interestingly, it is also found that impedance properties of micro‐ and nanopatterned Nafion thin films are associated with the Nafion polymer concentration and curing temperature. In particular, 20% Nafion thin films exhibit greater impedance stability and lower impedance values than 5% Nafion thin films at lower frequencies. Moreover, curing temperature‐specific impedance changes are observed. These results suggest that capillary lithography can be used to fabricate Nafion micro‐ and nanostructures with high pattern fidelity capable of modifying mechanical and electrical properties of Nafion thin films.