Electrokinetic concentration based on ion concentration polarization (ICP) offers a unique possibility to increase detection sensitivity and speed of surface-based biosensors for low-abundance biomolecules inside a microfluidic channel. To further improve the concentration performance, we investigated the effect of surface ion conductance of the ion-selective conductive polymer membrane, poly(3,4-ethylenedioxythiophene) polystyrenesulfonate (PEDOT:PSS), in a microfluidic channel. By increasing its thickness and surface charge, we could achieve a concentration increase of DNA by 6 orders of magnitude from an initial concentration of 100 fM within 10 min. As for the detection via surface hybridization on morpholino (MO) probes, DNA target concentration as low as 10 pM was detected within 15 min. This result means an improvement by 2 orders of magnitude in terms of the detection limit compared with our previous developed PEDOT:PSS membrane. These results demonstrate a potential application of the PEDOT:PSS membrane for the ICP-enhanced detection of DNA and other biomolecules in surface-based assays down to picomolar regimes.