Carboxylated polypyrrole (CPPy) nanotubes were fabricated by the chemical copolymerization of pyrrole and pyrrole-3-carboxylic acid (P3CA) using cylindrical micelle templates. Importantly, the chemical functionality of CPPy nanotubes was determined by the input amount of P3CA and their redox property was also retained without degradation. A field-effect-transistor (FET) sensor platform was constructed using liquid-ion gating. CPPy nanotubes were anchored on an amine-functionalized Au interdigitated microelectrode substrate to achieve high quality contact at the polymer/metal interface. Subsequently, heparin was covalently conjugated with the CPPy nanotubes via a diamino linker. The FET sensor based on heparin-conjugated CPPy nanotubes showed specific and fast response upon exposure to thrombin protein.