Yamaguchi began playing football in the third grade, playing mostly as an attacking midfielder. Upon entering junior high, he participated in trials with the Cerezo Osaka, Gamba Osaka and Kyoto Purple Sanga youth academies and ultimately joined the Cerezo Under-15 team, from whom he received an invitation on the spot. He enjoyed steady progress at the club, being selected to be part of the first entering class of the Japan Football Association Elite Program at the end of his first year. In 2006 Yamaguchi was promoted to the Cerezo Under-18 team, which later won the JFA Prince League U-18 in the 2008 season, in which he served as captain and was named league MVP.
Along with academy teammate Yusuke Maruhashi, Yamaguchi was promoted to the senior team in 2009, spending three months of the season training with the Palmeiras Under-21 academy. He was named to the Japan Under-21 team in his second season and played in all of the matches in a gold medal campaign at the 2010 Asian Games in Guangzhou.