Born to a Japanese father and a Swedish mother, he started his career with Rågsveds IF and stayed with the club until 1999 when he signed a contract with major Swedish club AIK. He made his debut for the club in the same year in Svenska Cupen as he came on as a substitute in the 80th minute against Gefle IF, he later came on as a substitute again in the final, which AIK won 1–0 against IFK Göteborg, making him the youngest in the country to win the Cup, being only 16 years and 364 days old.
His league debut was not until the 2000 season against his future club IF Elfsborg. He quickly established himself as a starting lineup player and really broke through as a player against Helsingborgs IF, a 4–1 victory, scoring a goal and making 2 assists. He missed out the first game of the 2001 season due to an injury he got during the pre-season, which would continue to haunt him for the rest of the season, but he fully recovered for the 2002 season. Prior to the 2004 season he was loaned out to Italian Serie B club Genoa over the spring part of the season, later when AIK was relegated to Superettan he signed with Norwegian club Vålerenga.
During the winterbreak of the 2003–04 season Genoa C.F.C. loaned Ishizaki until the end of the season. Ishizaki did not play many games for the club before returning to AIK. Genoa also had an option to buy the player, but it was never used.
Instead of following AIK down into Superettan, Ishizaki decided to sign with Norwegian club Vålerenga, helping the club to break rival Rosenborg BK 13 straight league wins and bringing the title back to the club for the first time since 1984.
He then left the club, signing for Allsvenska club IF Elfsborg.
Stefan Ishizaki returned to Sweden prior to the 2006 season, signing for IF Elfsborg. Being a major signing for the coming season, he helped the club to claim the league title at the end of the season.
After his successful first season he remained with Elfsborg, taking a medal every season, gold (1st) in 2006, bronze (4th) in 2007, the Stora Silvret (2nd) in 2008, Lilla Silvret in 2009 (3rd) and bronze (4th) in 2010. Prior to the 2010 season he signed a new 5-year contract with the club.
Stefan Ishizaki signed with the LA Galaxy in Major League Soccer before camps opened in January for the 2014 season. Ishizaki was released by the club on July 4, 2015 so he could return to Sweden to finish his career with his expectant wife.
On 10 July 2015, it was confirmed that Ishizaki signed a 2.5 year deal with AIK.As of 21 January 2017
AIK1999 Svenska Cupen Champion
Vålerenga2005 Tippeligaen Champion
IF Elfsborg2006 Allsvenskan Champion
2012 Allsvenskan Champion
LA Galaxy2014 MLS Cup Champion
2014 Western Conference (Playoff) Champion