Stacey Jones was born in Auckland, New Zealand, in 1976, a grandchild to New Zealand rugby league great Maunga Emery. Jones was a foundation member of the New Zealand Warriors in 1995 and became the club’s first player to be awarded life membership. Jones and the Warriors became inseparable and indistinguishable. During his time in the league, Jones was the whole package and the epitome of the number seven spot by solidifying his status as one of the best scrum-halves in the game.

He played junior grades for the Ponsonby Ponies and Mt Albert Lions before moving to the Pt Chev Pirates when he was nine. In 1994 he played for the Auckland City Vulcans side in the Lion Red Cup. In July 1994 he captained the Junior Kiwis as they toured Australia.

Jones was spotted by the new Auckland Warriors franchise and made his first grade debut in 1995 against the Parramatta Eels in their inaugural year. On 23 April 1995 Jones made his first-grade début in Sydney, coming off bench to score a try in the Warriors 40–4 win over the Parramatta Eels. Greg Alexander missed Rounds 10 and 11 through injury which resulted in Jones taking over at halfback. Jones played well enough to retain the position and force Alexander to move to fullback upon his return.

Over the next several years Jones cemented his spot in both the Warriors and Kiwis, sticking with the Warriors despite the lack of success on and off the field. Between 1995 and 1999 he played over 100 consecutive first grade games for the Warriors. In 1999 he broke his arm playing for the Kiwis against Tonga, and as a result missed the first half of the 2000 NRL season, breaking his consecutive streak. At the end of 2000 the Warriors were sold for the second time in their short history. Jones was the first signing by the new franchise, and it was his commitment that convinced many other players to re-sign with the club.

In the three-year period 2001-03 he led the Warriors to 3 successive finals appearances. In 2002 the club not only won the Minor Premiership, but also reached the 2002 NRL grand final against the Sydney Roosters. Playing at scrum half back, Jones captained the losing side that evening but scored a brilliant individual try in which he beat three Roosters defenders from 30 metres out to go over from dummy half. He was then selected to go on the 2002 New Zealand rugby league tour of Great Britain and France and won the George Smith Medal as player of the series against Great Britain. Also in 2002, Jones became only the second New Zealand player to win the Golden Boot Award for the best international rugby league player.

In his career, he has also represented New Zealand at two World Cups (1995 and 2000), three Tri Nations series (1999, 2005, 2006), playing 41 games for the New Zealand Kiwis. He retired from the national team in 2004 while having a disappointing year at club level. However, on 15 October 2005 Stacey ended 2 years of retirement, answering an SOS from Kiwis coach Brian McClennan intending only to play the Australasian section of the Tri Nations series. He then went on to play the rest of their round robin matches against Great Britain in England. Stacey Jones was an integral part of the New Zealand Tri Nations campaign. In the first match, he guided the Kiwis to their first win in Sydney in 50 years before being part of their narrow loss to Australia in Auckland. He set up 4 tries in the first match in England which the Kiwis won by 42–26.

In April 2005 Stacey Jones announced he was leaving the Warriors, then his only professional club to join the new French addition to the Super League for the 2006 season Catalans Dragons. In doing so he became the last foundation member of the Warriors to leave the club. Jones helped Catalans reach the 2007 Challenge Cup Final. In September 2007 he announced his retirement from the game and left the Dragons.

Stacey Jones returned home and rejoined the New Zealand Warriors as their kicking coach for the 2008 season. As part of his release from the Dragons he was not allowed to play for any other club during the 2008 season. In November 2008 it was announced that Stacey Jones had re-signed as a player with the New Zealand Warriors on a one-year contract for 2009. He reportedly signed a contract worth over $220,000. In his March 2009 return game to the NRL, Jones set up two tries and guided his team to a 26–24 victory over Manly, reaffirming his nickname as "The Little General". Unfortunately, Jones' early good form did not continue and the Warriors struggled to a disappointing 14th placing on the ladder. In early September Jones announced that his comeback was over and he would not be returning for the 2010 NRL season.

In 2015 Jones coached the Warriors side in the NSW Cup. Jones was subsequently an assistant coach for the Warriors in various capacities under coaches; Andrew McFadden, Stephen Kearney, Todd Payten and Nathan Brown. In 7 June 2022, Jones was named interim head coach of the New Zealand Warriors after the sudden departure of coach Nathan Brown who refused to commit to the club long term. On 21 February 2024, Jones was named head coach of the New Zealand national rugby league team, replacing Michael Maguire who left the position to coach New South Wales.