Nanopore sensing measures the changes in charge and physical state around the nanopores as changes in ionic current. In this study, we performed vancomycin (VCM) sensing with nanopores modified via Au−S bonds with dithiobis(4‐butyrylamino‐m‐phenylboronic acid) (DTBA‐PBA), a derivative of phenylboronic acid (PBA) bearing a thiol. First, we modified a 3‐mm‐diameter Au electrode with a DTBA‐PBA self‐assembled monolayer (SAM) to confirm the VCM response of the PBA interface by cyclic voltammetry. DTBA‐PBA was then immobilized in the same manner on a nanopore pipette coated with an Au layer. We measured the VCM concentration from the change in ion current using the nanopore pipette. A VCM concentration‐dependent ionic current response was observed in the range of 0.01–1 mM. Many kinds of pharmaceuticals can bind to PBA; therefore, this method could be used for quick, easy, in situ quantification of not only VCM but also other pharmaceuticals with serious side effects.