Heat transfer enhancement is an important issue in energy systems. To improve the efficiency of a cooling channel used inside injection molds, turbine blades, and high-temperature devices, channels with various shapes, such as wavy, elliptical, and twisted, have been studied. A cooling channel with a partially wavy inner structure has shown outstanding cooling performance despite a small increase in friction factor. However, generating a partially wavy inner structure inside a channel through conventional machining processes is not easy. To address this problem, we developed a new process called Perpendicular vibration-induced electrical discharge machining (PV-EDM). A specific electrode and one-and random-directional vibrating devices controlled by a pneumatic load were designed for the PV-EDM process. Experimental results showed that local shaping on the inner wall of a channel is possible, which confirmed the possibility of application of this process to actual industrial problems.