Zhao Junzhe graduated through Liaoning FC youth team making his professional debut in the 1999 season where he played in 25 games and scoring 3 goals. He has continued to be a vital member for Liaoning FC where he aided them to a runners-up position in the League table and Chinese FA Cup. He would eventually become the teams captain and even personally win the Chinese Football Association Footballer of the Year award in 2004. The following seasons saw the clubs fortunes fall and Zhao Junzhe unfortunately led the team to relegation to the second tier at the end of the 2008 league season. Despite this he remained with the team and immediately led them back up to the top tier when he led the team to win the division title in 2009.
China's club coaches initially pushed for the inclusion of Zhao in the country's national set-up and Bora Milutinović eventually included him in his 2002 FIFA World Cup squad. Though his chances were limited so far on the international team he did play in two World Cup games during the tournament and nearly scored by hitting the post against Brazil. He has since been included in several unsuccessful squads and played a vital role in the 2004 AFC Asian Cup which China were runner-up. However since the arrival of Zhou Haibin, Zhao has found it difficult to be selected within midfield and did not play in the 2007 AFC Asian Cup with Zhou Haibin preferred.