A New Zealand national captain and second-row forward, Kearney's club football career, which spanned from the early 1990s to the mid-2000s, was played for the Randwick Kingfishers, Western Suburbs Magpies, Auckland Warriors, Melbourne Storm (with whom he won the 1999 NRL Premiership), and Hull F.C. (with whom he won the 2005 Challenge Cup).
A Kapiti Bears junior, Kearney played for the Junior Kiwis between 1989 and 1991, becoming the side's captain for the 1991 series against Great Britain. He made his senior début in 1991 for the Randwick Kingfishers and also played for Wellington that year. Randwick lost the Wellington Rugby League Grand Final 6-14 to the Wainuiomata Lions.
Turning professional he moved to Australia to play for the Western Suburbs Magpies in 1992 in what is now the NSWRL Premiership. In 1993 he became the New Zealand Kiwis' youngest test captain, aged 21. He left the Magpies at the end of 1994, returning home to play for the Auckland Warriors in their inaugural season. At the end of that season he traveled to England to represent New Zealand in the 1995 World Cup. He missed the first test match against a re-unified Australian team in 1998 due to suspension. Kearney remained a Warrior until 1998, when he moved to Australia to join the Melbourne Storm. In the Melbourne club's second ever season Kearney played at second-row forward in their victory in the 1999 NRL Grand Final. Kearney was selected for the New Zealand team to compete in the end of season 1999 Rugby League Tri-Nations tournament. In the final against Australia he played at second-row forward in the Kiwis' 22-20 loss.
Having won the 1999 Premiership, the Melbourne Storm traveled to England to contest the 2000 World Club Challenge against Super League Champions St Helens R.F.C., with Kearney playing at second-row forward in the victory. In 2002 Kearney missed the series-deciding match against Great Britain as he had to rush back home to Melbourne to be with his sick five-year-old daughter, who needed emergency surgery. While captaining the Storm in 2004, Kearney became the first New Zealand footballer to play 250 Australian first-grade matches. He also played his last test match for the Kiwis in 2004, in a game that marked the début of Sonny Bill Williams. Kearney finished his playing career with English club Hull F.C. in Europe's Super League competition, playing in their 2005 Challenge Cup-winning side.
In 2006 Kearney retired and returned to Australia to take up a role as assistant coach at his old club, the Melbourne Storm, under Craig Bellamy. In 2008 Kearney was appointed as the New Zealand Kiwis' head coach on a two-year contract.
Kearney (with assistant Wayne Bennett) coached the Kiwis to their first World Cup series win. On 22 November 2008, they defeated Australia 34–20 in the final, at Suncorp Stadium in Brisbane. Following this achievement, he was made an Officer of the New Zealand Order of Merit in the Queen's Birthday honours list.
For the 2010 Anzac Test, Kearney coached New Zealand in their loss against Australia. In the 2010 post-season Kearney was announced as Daniel Anderson's replacement as head coach of the Parramatta Eels for three years beginning in 2011. Shortly after that, he took the Kiwis to victory in the 2010 Four Nations Final against Australia.
In 2011 he failed to coach the Parramatta NRL team to any success, with the Eels achieving just 6 wins and 1 draw in 24 matches, and only just missing out on the wooden spoon when they beat the Gold Coast Titans in the last game of the regular season.
Things didn't get any better for Kearney in the 2012 NRL season. With the Eels struggling in last place on the NRL ladder after 16 rounds, Melbourne Storm's inaugural coach, and two time premiership winning coach Chris Anderson was appointed as a mentor to Stephen Kearney to help him turn the club's fortunes around. However this did not eventuate as Kearney was eventually forced to resign only three rounds later on 20 July, after achieving only 3 wins from 19 matches in the season. He left the Eels with just 10 wins from 42 matches, for a poor winning percentage of 24 percent.
In October 2012 Kearney signed 2 years as Brisbane Broncos assistant coach from 2013.
In November 2014, Kearney guided New Zealand to their second Four Nations championship, defeating Australia 22-18 in the final.
In March 2015, Kearney signed a new deal to remain as coach of the Kiwis until the conclusion of the 2017 Rugby League World Cup.
At the end of 2015, his 23 test wins as coach and five wins over Australia is the most out of any that has coached New Zealand in the past.
On 12 September 2016, Kearney stepped down from his role as coach of New Zealand after accepting to return to head coaching in the NRL as coach of the New Zealand Warriors on a three-year deal.
In 2012 Kearney was named as one of the New Zealand Rugby League's Legends of League. He was also named in the Wellington Rugby League's Team of the Century.