O'Neill has had considerable success with Tyrone youth teams winning 2 Ulster and All-Ireland under 21 titles in 2000 and 2001 to add to his Ulster Minor championship medals in 1997 and 1998 and his All-Ireland minor championship in 1998.
Senior
O'Neill burst on to the senior county scene and by 2001 had won an Ulster title and the first of his three All Star Awards. During his time with Tyrone he was first choice penalty taker – scoring three in the run up to Tyrone's 2005 All-Ireland victory, and also shared free-taking duty with Eoin Mulligan—usually dictated by who is kicking on their stronger side. O'Neill won All-Ireland Senior Football Championship medals with Tyrone in 2003 and 2005, and the National Football League in Tyrone's break-through year of 2002, and again in 2003. Serious injury ruled him out for much of Tyrone's unsuccessful 2006 championship. He won an All Stars Award in 2001 and 2005. In 2005, he was won a clean sweep of the Texaco award, the Gaelic player's award and the Vodafone award for Footballer of the Year, after a monumental year where he scored a total of 64 points. These performances earned him a place in the Irish team in the international rules series for 2005 against Australia.
Retirement and return
Following two years where he was blighted by recurring injuries, O'Neill agreed to undergo surgery before the end of 2007 to resolve a complex knee tendinitis condition. It was hoped that this would make him fully fit for the 2008 Championship, but he is now retiring from county football at the young age of 27. However, on 4 September 2008, it was announced that O'Neill would be available for selection for the All-Ireland final, following the approval of the other panel players who had reached the final without his contributions. This was despite the fact that a mere two days earlier he had gone on record denying a return, suggesting that his long absence would affect his match-sharpness. O'Neill's return to action came earlier than many expected during the 2008 All-Ireland Senior Football Championship Final, as a 25th minute sub for the injured Colm McCullagh. Although he failed to register a score he caused the Kerry defence a number of problems and helped Tyrone to their third Senior Football Championship win in six years. Despite being entitled to one, O'Neill refused to accept his winner's medal, saying that he "did not earn" it. He was visibly upset as he was climbing the steps to be presented the trophy, and had to be consoled by teammates, such as Dave Kitson. O'Neill helped Tyrone win another Ulster Championship in 2009, beating Antrim in the final, collecting an end of season All Stars Award, his third. O'Neill dislocated his elbow in the final of the 2010 Dr. McKenna Cup, which Tyrone lost to Donegal.
Club
Stephen's home club is Clan na Gael in Aughabrack. With the side he has won one Tyrone Junior Championship and one Tyrone Intermediate Championship.