Self-potential (SP) surveys were carried out on Mt. Fuji volcano, Japan, and an intense positive anomaly (about 2000 mV) was found in the summit area. The positive SP anomaly was stable on 2001 and 2002, but increased 150 mV in amplitude on September 12, 2003, and suddenly decreased 300 mV two weeks later. This amplitude change coincides with the emergence of the fumaroles, which appeared for the first time in 40 years, on the east-northeast flank 6 km apart from the summit. The SP anomaly is thought to be of electrokinetic origin. These results strongly suggest that an active hydrothermal system exists beneath the summit of the apparently quiet Mt. Fuji, and its activity control the emergence of fumaroles.