Stockton is considered one of the NBA's greatest point guards as he averaged a career double-double, with 13.1 points and 10.5 assists per game. As of 2005, he held the NBA's records for career assists (15,806) and career steals (3,265). He had five of the top six assists seasons in NBA history. He has held the NBA record for the most seasons and consecutive games played with one team, and is second in total games played. He missed only 22 games during his career, 18 of them in one season.

In Stockton's 19 year career, he appeared in 10 All-Star games, and was named co-MVP of the All Star Game in 1993.. He played with the 1992 and 1996 US Olympic basketball teams, known as Dream Teams I and II, the first Olympic squads to feature NBA players. He was selected to the All-NBA First Team twice, the Second Team six times, the Third Team three times, and the All-Defensive Second Team five times. He was named one of the 50 Greatest Players In NBA History in 1996. Stockton's career highlight came in Game 6 of the Western Conference Finals, in which he hit the winning shot over Houston to send the Jazz to its first NBA Finals.

Stockton announced his retirement in May of 2003. The Jazz later held a retirement ceremony for him, in which Salt Lake City renamed the street in front of the Delta Center, where the Jazz play, "John Stockton Drive." His number 12 jersey was retired by the Jazz during a game on November 22, 2004. A statue of Stockton can be seen in front of the Delta Center.

On April 6, 2009, Stockton was inducted into the Naismith Memorial Basketball Hall of Fame.