Whelan revealed he had held out for Leeds to sign him (the club he supports) after having trials at Arsenal, Manchester United, and Everton,[4] coming through the Leeds youth team with a number of other talented youngsters who beat a Manchester United team boasting David Beckham, Paul Scholes, Nicky Butt, Keith Gillespie, Phil Neville and Gary Neville both home and away in the FA Youth Cup Final.
On 16 December 1995, after making eight goalless appearances in the league 1995–96 season,[5] Whelan was signed by Coventry City manager Ron Atkinson for £2million.
Atkinson's assistant Gordon Strachan, who had joined Coventry from Leeds the previous season, played a big role in securing the signing.
In his second game, against Everton at Coventry's Highfield Road stadium, Whelan played as a striker alongside Dion Dublin, and scored the winning goal with a cool finish, which would become his trademark for the rest of the season.
The Sky Blues' form improved markedly in the 1997–98 season as they rose to mid-table respectability in the Premiership under manager Gordon Strachan, with Noel Whelan playing a key role in midfield.
Back in an attacking position, Whelan struck up a good partnership with Darren Huckerby, bringing his best goal return (10 in 31 Premier League games) in the process, and prompting some Coventry City fans to demand his inclusion in the England national team squad.
Coventry fans were expecting a great deal of the Whelan-Huckerby partnership in the 1999–2000 season but were to be disappointed as first Whelan sustained a bad injury in pre-season and Huckerby was sold to Leeds United.
Whelan would miss most of the first half of the season as Gordon Strachan built an exciting new team featuring Robbie Keane, and the Moroccan duo Moustapha Hadji and Youssef Chippo.
He did, however, enjoy a brilliant run of form, possibly the best of his career, which includes a goal against Manchester United in the FA Cup fourth round in Middlesbrough's 2–0 victory, after which he celebrated by simply giving the "Leeds Salute", because of his love of the West Yorkshire club and their bitter rivalry with his opponents that day.
The goalless spell at Derby saw Whelan sign for Scottish club Aberdeen[8] at the start of the 2004–05 season and he would score five times in twenty appearances for the Pittodrie side.
His one-year contract passed without renewal and Whelan moved back to England to start the 2005–06 season at Football League Two club Boston United, where he scored four goals in fifteen games.
[11] The following day's papers linked him with a move to First Division leaders Gretna to spearhead them in their charge for Scottish Premier League football.
[12][13] In October 2009, Whelan joined League Two's bottom-placed side Darlington on non-contract basis, to become new manager Steve Staunton's first signing.
On 31 January 2018, Whelan also featured in a two part documentary exclusive to Leeds United's TV channel LUTV called 'I Wore The Shirt'.