Motohiro Yamaguchi started his professional career with the company football team of All Nippon Airways (the later Yokohama Flugels) in 1991 through Maebashi Ikuei high school and Tokai university.
He won the Emperor’s Cup in 1993 and he was awarded the best eleven of J.League in 1996 and 1997. After the shocking announcement about merger of Yokohama Flugels and Yokohama Marinos in October 1998, Yamaguchi led the team as a skipper and Flugels won all remaining J.league and the Emperor's Cup matches, then finally the team was dissolved at the end of the season as champions of the Emperor's Cup.
 
From 1997 to 2002, Yamaguchi played for Nagoya Grampus, won several titles. 
In 2003, he moved to J2 side Albirex Niigata and captained the team and promoted to the top division. 
In August 2005, he was transferred to Yokohama FC. He repeated his achievements made in Niigata there as well, led the club to J1 in only one year as a skipper.  
He also was an essential player of the national team during the late 90s and played in FIFA World Cup 1998, appeared in all 3 Japan’s matches. 
After retirement, he worked as a TV commentator for several years, then decided to start his coaching career and was appointed as a manager for his former club Yokohama FC in March 2012.
He led the team from the bottom of the division 2 table to 4th place at the end of 2012 season. 
In 2016, he managed U-17 national team in international tournaments as a manager.
Since 2018 Yamaguchi has joined Nagoya Grampus, worked as an academy director, the Head of Football and now works as the General Manager.