Then purchased by Ipswich Town, he made over 100 appearances for the club before earning a big money move to Crystal Palace.

After returning from a loan spell at Norwich City, he wrote himself into the club's folklore by scoring in the final game of the 2009–10 season against Sheffield Wednesday, saving the Eagles from relegation and ultimately administration.

He joined Torquay United on loan on 27 November 1998 and made his debut the following day in the Third Division in a 3–1 defeat to Barnet at Underhill; he replaced Tony Bedeau as a substitute at half-time.

He scored his first league goal on boxing day, which secured a 1–1 draw with Exeter City at St James Park.

[2] Making 11 appearances, he scored in draws with Bradford City and Tranmere Rovers, helping the "Valiants" to avoid relegation out of the First Division on goal difference.

In his first season at the club, 2000–01, he scored 15 goals in 35 games as Ronnie Moore's "Millers" won promotion out of the Second Division as runners-up.

[7] He remained a key fixture at Millmoor in the First Division, scoring ten goals in 41 games in 2001–02, and finding the net 16 times in 44 appearances in 2002–03.

He ended the 2006–07 campaign with 17 goals in 44 games, including a header that relegated Leeds United on the last day of that season.

On 30 January 2011, he scored his first goal for Huddersfield in an FA Cup Fourth Round 2–1 defeat to Arsenal at the Emirates Stadium.

[27] He finished the 2011–12 campaign with seven goals in 38 games and was an extra time substitute in the play-off final victory over Sheffield United at Wembley Stadium, though missed his penalty in the shoot-out.

[28] Lee scored his first goal of the 2012–13 season in a 3–2 home defeat by Watford after replacing newly signed emergency loanee Jermaine Beckford.

Lee returned to Ipswich Town in July 2013 as part of the club's academy staff and later began training with the first team after Mick McCarthy considered handing him a first-team contract.

[31] He re-signed as a player on non-contract terms on 30 August, allowing him to play in the club's first-team whilst retaining his academy coaching position.

[32] He made an appearance in the FA Cup, coming on as a late substitute in a 3–2 defeat to Preston North End on 14 January.