Ion-selective electrodes (ISEs) are widely used to detect targeted ions in solution selectively. Application of an ISE to a small area detection system with a nanopipette requires a special measurement method in order to avoid the enhanced background signal problem caused by a cation-rich layer near the charged inner surface of the nanopipette and the selectivity change problem due to relatively fast saturation of the ISE inside the nanopipette. We developed a novel ion-selective detection system using a nanopipette that measures an alternating current (AC) signal mediated by saturated ionophores in a poly(vinyl chloride) (PVC) membrane located at the conical shank of the nanopipette to solve the above problems. Small but reliable K⁺ and Na⁺ ionic current passing through a PVC membrane containing saturated bis(benzo-15-crown-5) and bis(12-crown-4) ionophore, respectively, could be selectively detected using the AC signal measurement system equipped with a lock-in amplifier.