Endo was born in Kagoshima on January 28, 1980. After graduating from Kagoshima Jitsugyo High School, he joined J1 League club Yokohama Flügels in 1998. In March, he debuted against Yokohama Marinos in opening game in 1998 season. He played many matches as central midfielder in 1998 season. The club won the champions in 1998 Emperor's Cup. However the club was disbanded end of 1998 season due to financial strain. In 1999, he moved to Kyoto Purple Sanga with contemporaries Kazuki Teshima, Hideo Oshima and so on. He became a regular player and played many matches. However the club was relegated to J2 League end of 2000 season.