A simple two-step electrochemical method is proposed for the synthesis of nanowire-based polypyrrole hierarchical structures. In the first step, microstructured polypyrrole films are prepared by electropolymerization. Then, polypyrrole nanowires are electrodeposited on the surface of the as-synthesized microstructured polypyrrole films. As a result, hierarchical structures of polypyrrole nanowires on polypyrrole microstructures are obtained. The surface wettabilities of the resulting nanowire-based polypyrrole hierarchical structures are examined. It is expected that this two-step method can be developed into a versatile route to produce nanowire-based polypyrrole hierarchical structures with different morphologies and surface properties.