Lee has won the Football League Trophy with Doncaster Rovers, and helped both Hartlepool United and Sheffield Wednesday to promotion in the mid-2000s.

[5] Sheffield Wednesday won promotion to the Championship after defeating former club Hartlepool United in the 2005 play-off final, however, Lee missed the match.

Lee was deemed as not good enough for the Championship following the side's promotion by Paul Sturrock and signed for Doncaster Rovers from Sheffield Wednesday for £50,000 in 2005.

[14] Two weeks later he added a second goal, helping City to upset League One-side Milton Keynes Dons 2–1 in the FA Cup.

[16] Lee signed a two-year deal for Notts County joining on a free transfer on 30 June 2009[17] just prior to the infamous takeover of the club by Munto Finance.

Lee played an important role as County were promoted as Champions of League Two in 2010 under Ian McParland, Sven-Göran Eriksson, Hans Backe, Dave Kevan and Steve Cotterill.

Darlington suffered financial difficulties during Lee's time at the club and his contract was terminated on 16 January 2012, along with the rest of the playing squad and caretaker manager Craig Liddle.

[18] However, despite the ongoing financial and contractual issues at Darlington, Lee continued to play on until a knee injury ruled him out for the remainder of the season.

[3] However, it was the downturn in form following the defeat to Rotherham that was citing in Lee losing his job with the club only winning once out of their previous eleven games.

[24] Despite a slow start to his tenure in charge, Lee turned around the club's form, leading them away from the relegation zone, earning the league's Manager of the Month award for February 2024.