Whelan started his career at Manchester City but only made one appearance which came in the UEFA Cup and after a loan spell at Bury he moved on to play for Sheffield Wednesday, with whom he won promotion to the Championship in May 2005.

He took a while to establish himself in Tony Pulis' first team plans in the top flight but by 2009 he became a regular and went on to play in the 2011 FA Cup final, but his old club Manchester City beat Stoke 1–0.

Whelan spent nine years at Stoke making 338 appearances before joining Aston Villa in July 2017 and then Hearts in August 2019.

[8] He made a solitary appearance in the UEFA Cup coming on as a substitute for Paul Bosvelt against Total Network Solutions in August 2003,[9] before joining Bury on a one-month loan the following month.

[11] In total Whelan played 15 times on loan at Bury and caught the attentions of Sheffield Wednesday manager Chris Turner.

[13] He made his debut for Wednesday against Huddersfield Town on 21 August and in his next match, a League Cup tie against Walsall, he provided Lee Peacock with an assist and earned the praise from his manager.

[16] His promising start to his Wednesday career took a knock as he was sent off in a League Cup tie against Coventry City for "violent conduct".

Whelan was voted "man of the match" in the League One play-off final against Hartlepool United at the Millennium Stadium in Cardiff after scoring the match-winning third goal for Wednesday.

[21] Wednesday were able to avoid an instant return to the third tier in 2005–06 as they finished in 19th position, Whelan playing in 46 matches that season scoring once, which came in a 2–1 defeat against Watford.

[42] After drifting in and out the starting eleven for most of the 2010–11 season Whelan made a return in March and played a key role in Stoke's run to their first FA Cup Final.

[47] In a match against Bolton Wanderers referee Howard Webb awarded an indirect free-kick inside the penalty area for a back-pass against Whelan after two minutes.

[49] In January 2012, manager Tony Pulis confirmed that he wanted Whelan to sign a new contract stating "Every time you ask Glenn to step up to that next level, he does it.

[50] Whelan signed a new three-and-a-half-year contract on 11 January 2012 and said "I am loving life at the moment and things are going really well, so I am absolutely delighted to commit my long-term future to the club".

[57] At the end of the 2012–13 season Tony Pulis was replaced by Mark Hughes and Whelan stated that he hopes the change in style of play will help the team score more goals.

[61] Whelan retained his place in the side at the start of the 2014–15 season before he was ruled out of six weeks suffered a fractured leg whilst on international duty with Ireland in October 2014.

[65] Whelan played 30 times for Stoke in 2014–15 as the Potters finished in 9th position for a second season running and they ended the campaign with a 6–1 victory against Liverpool.

[73] Prior to the start of the 2016–17 season, Whelan signed a one-year contract extension in July 2016, which ties him to Stoke until the summer of 2018.

[80] Whelan played 35 times in 2017–18 helping Villa reach the 2018 EFL Championship play-off final where they lost 1–0 to Fulham.

[87] Whelan signed a short-term deal with League One club Fleetwood Town on 24 January 2020, joining until the end of the season.

[92] This was initially thought to be his last match for the club as he was released at the end of the season,[93] but he returned to Rovers just a few weeks later on 29 July 2022 in the role of first-team coach, also being registered as a player if he were to be required.

[96] In October 2000, Whelan played for the Republic of Ireland under-16 national team in a qualifying tournament in Riga for the 2001 UEFA European Under-16 Championship where he came up against Andrés Iniesta.

[97] Whelan made his debut for the senior team against Serbia in May 2008[98] and scored his first international goal against Georgia in Mainz, Germany on 6 September 2008.

[99] Since the appointment of Giovanni Trapattoni, Whelan became a key member of the squad and made 11 straight appearances despite previously being considered an "also-ran".

[105] He was branded a "terrible" player by RTÉ pundit and former Republic of Ireland international Eamon Dunphy in the aftermath of a poor performance in a 2014 FIFA World Cup qualifying match against Sweden.