Born in Leeds, Whelan started off with his professional career at home town team Leeds United. Whelan revealed he had held out for Leeds to sign him (the club he supports) after having trials at Arsenal, Manchester United, and Everton F.C., 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 F.A. Youth Cup Final. Turning professional in March 1993, he made his debut in the first season of the FA Premier League, in a 1–1 draw at Sheffield Wednesday on 4 May 1993. The following season, he made 16 league appearance but failed to score.

He had a promising 1994–95 season, finishing among the club’s highest scorers where he scored seven goals in 23 league games, but lost his place to new signing Tony Yeboah halfway through the season. During his time at Leeds, he was capped twice by the England U-21 side in 1994, scoring once.

On 16 December 1995, after making eight goalless appearances in the league 1995–96 season, 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. Whelan made his debut in midfield in a 4–1 local derby defeat against Aston Villa at Villa Park. 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. Further goals came in the away win at Burnden Park against Bolton Wanderers, and in the New Year’s Day home draw with Southampton. The latter was a “Goal of the Month” contender on the BBC’s Match of the Day. It saw Whelan dribble the ball from just inside the Southampton half, and beat several players before shooting past the keeper. By the end of that season, he had managed eight goals from 21 league games for the Sky Blues, who secured Premier League safety by finishing 16th.

On 4 August 2000, Whelan was sold to Bryan Robson’s Middlesbrough for £2.2million. His debut was at Highfield Road as a substitute in Boro’s 3–1 victory on the opening day of the 2000–01 season. The three-year spell with Boro would be the last time Whelan would feature prominently for a club for more than one season. 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. He also scored an own goal against his former club Coventry on his 26th Birthday. The match ended up in a 1–1 draw. He had limited chances in the league, though, appearing in just 19 out of Middlesbrough’s 38 Premier League matches in the 2001–02 season, scoring four times. He would appear 15 times for Middlesbrough in the 2002–03 league campaign, scoring once.

Whelan stayed in the Scottish Premier League, as he signed a one-year contract with Dunfermline Athletic in July 2006, making his first competitive start on 29 July against Heart of Midlothian in a 2–1 defeat. Unfortunately, he had to leave the field injured after just three minutes. After six months out injured Dunfermline terminated their contract with Whelan by mutual consent on 4 January 2007. 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. Since then Whelan has assisted in coaching at Dunfermline, whilst studying for coaching badges; he is said to be interested in a career in management.

He joined Conference North side Harrogate Town on 11 December 2008.

Whelan competed in an episode of Celebrity MasterChef broadcast in 2008, but was eliminated in the first round.

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. He made his debut for Darlington against third-placed Dagenham & Redbridge on 10 October but he was substituted by Curtis Main before half-time because of a muscle strain injury, in a game which Darlington lost 2–0. He did not play again for Darlington until 26 January, more than three months after his debut, when he came on as a second-half substitute against Northampton Town. However, his comeback lasted only two minutes, before he himself was substituted because of a hamstring injury.

On 17 November 2010, Whelan revealed he has put his name forward for a role working within Leeds United’s academy. Leeds are the club who Whelan supports and also who gave him the chance to become a professional footballer.

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’.

In April 2019, Whelan joined EFL Championship side Leeds United as a coach for Leeds United Development Hub for elite player development scholarship.