McDonnell joined the Glen Rovers club at a young age and played in all grades at juvenile and underage levels. On 20 November 2005, he was at midfield when Glen Rovers defeated Carrigaline by 0-15 to 1-08 in the Premier County Minor Championship final. On 11 November 2006, McDonnell was again at midfield for a second successive Premier County Minor Championship final. Bishopstown were the opponents, however,0-12 from Patrick Horgan secured an 0-18 to 2-09 victory. McDonnell subsequently progressed onto the Glen Rovers under-21 team. On 8 November 2008, he was at left wing-back when Glen Rovers drew with Duhallow in the Cork Premier Under-21 Championship final. The replay took place on 16 November, with Glen Rovers winning by 4-15 to 2-18.
Senior
On 10 October 2010, McDonnell lined out at full-back in Glen Rovers' first Cork Senior Championship final in 19 years, however, Sarsfields won the game by 1-17 to 0-18. On 12 October2014, McDonnell was again at full-back when Glen Rovers faced Sarsfields in the Cork Senior Championship final. After helping to set up the Glen's opening score, the team suffered a heavy 2-18 to 0-08 defeat. McDonnell was at right corner-back for much of the Glen's 2015 championship campaign. He was also named in that position for the final against reigning champions Sarsfields, with the Glen winning by 2-17 to 1-13. It was the club's first championship title since 1989. For the third year in-a-row, Glen Rovers qualified for the championship final on 9 October 2016. McDonnell was at full-back in the 0-19 to 2-10 defeat of Erin's Own. On 20 October 2019, McDonnell played in his fifth final when Glen Rovers faced Imokilly. Lining out at right corner-forward, he ended the game on the losing side following a 2-17 to 1-16 defeat.
Cork
Minor and under-21
McDonnell first played for Cork at minor level during the 2007 Championship, a year which also saw him captain the team. He made his first appearance on 2 May when he played at left wing-back in Cork's 3-15 to 0-09 defeat of Waterford. On 8 July, McDonnell was at midfield for Cork's 0-18 to 1-11 Munster Championship final defeat by Tipperary. After being substituted in that game, he was dropped from the starting fifteen for the subsequent All-Ireland Championship and replaced as captain by Ryan Clifford. On 2 September, McDonnell started the All-Ireland final against Tipperary on the bench but was introduced as a 24th-minute substitute in the 3-14 to 2-11 defeat. On 2 June 2010, McDonnell made his first appearance for the Cork under-21 team in a 1-16 to 1-03 defeat of Waterford in the Munster Championship.
Senior
McDonnell made his first appearance for the Cork senior hurling team on 13 February 2011 in a 1-20 to 1-15 National Hurling League defeat of Offaly at Páirc Uí Chaoimh. He was later included on Cork's panel for the 2011 Munster Championship and made his debut at right corner-back on 29 May in a 3-22 to 0-23 defeat by Tipperary. On 6 May 2012, McDonnell lined out at full-back in the National League final. Cork eventually lost the game to Kilkenny by 3-21 to 0-16. McDonnell lined out in his first Munster Championship final on 14 July 2013, however, Cork suffered a 0-24 to 0-15 defeat by Limerick. On 8 September, he lined out at right corner-back against Clare when the sides drew in the All-Ireland final. McDonnell was again at right corner-back for the replay on 28 September which Cork lost by 5-16 to 3-16. On 3 July 2014, McDonnell won a Munster Championship medal following Cork's 2-24 to 0-24 defeat of Limerick in the last final to be played at the old Páirc Uí Chaoimh. He ended the season by being nominated for an All-Star. On 3 May 2015, McDonnell was at left corner-back in Cork's 1-24 to 0-17 defeat by Waterford in the National League final. On 3 November 2016, McDonnell was appointed captain of the Cork senior hurling team. His season as captain ended with a first championship defeat for Cork by Wexford in 60 years. McDonnell retained the captaincy of the team for the 2007 Championship. He won his second Munster Championship medal on 9 July following a 1-25 to 1-20 defeat of Clare in the final. In December McDonnell announced that he was leaving the Cork panel. New manager John Meyler said: "Stephen’s not in our plans. He’s taking time out in 2018 so he won’t be available." It was announced in November 2018 that McDonnell would be returning to the Cork panel for the 2019 season.
