Lee Blackburn played for Norwich's Under-19s in their 3-1 victory over Millwall on 9th March 2002. Lee scored twice. He followed this up with an "impressive game in midfield" for the Under-17s in their 5-1 victory over Danish side Lyngby at Easter 2002.

That was the start of Lee's second spell with the Canaries. He was with Norwich's centre of excellence at Potters Bar until new FA rules closed the centre in 1998. He joined Chelsea for four years but on his release from Stamford Bridge, Norwich offered him an academy contract as they knew what he was capable of doing on the pitch.

He was described by Sammy Morgan in the summer of 2003 as "a terrier of a player with great energy and competitive edge. Put in some very good performances in the second half of last season. Understands his role and is channelling his energies in the correct departments". Lee won the FONCY (Friends of Norwich City Youth) Player of the Year award for 2003/4

On January 26th 2005, Norwich announced that they would not be offering professional contracts to third year scholars .Adam Smith, Lee Blackburn, Olly Willis and Nicky Howell. "We've worked with the boys and when it comes to the crunch, a decision has to be made," said Nigel Worthington. "Unfortunately, from their point of view, the boys will not be taken on. We will do everything we can to help them move forward, whether that be in football or another field". Ricky Martin added the timing of the decision was made to give the players the chance to make other plans. "We've looked to make this decision at this time to enable the players to finish off the educational element of their scholarship and to make a decision as to whether to pursue their career with trials at another football club or to apply to university."

After a trial with Notts County reserves against Darlington Reserves (9th February) alongside Kidderminster Harriers duo Steve Burton and Youssou Diop, Lee switched his scholarship to Cambridge United in the middle of February 2005. This lasted until the end of the season and enabled Lee to play for the struggling Division Two side. Lee made his Football League debut for the struggling Cambridge team. Although Cambridge were relegated and subsequently released 12 of their squad, Blackburn was offered a professional contract in May 2005. Their financial plight and adminsitration prevented this from materialising, and in July, Lee could be found playing for Crawley against Millwall in a pre-season friendly. At the beginning of August 2005, Lee signed a two year deal with Crawley.

Kings Lynn manager Tommy Taylor revealed in June 2006 that Lee had been invited to spend pre-season training with the Linnets. Taylor also confirmed former Norwich City youth product Lee Blackburn had been offered a fresh deal by cash-strapped Conference club Crawley. "Lee has a decision to make," he said. "The lad has a tremendous pedigree but he needs to sit down and do what is best for him. I want plenty of different options in midfield and he could do us a job."

Lee remained at Crawley until May 2008 when he was released as he had lost his place in the Crawley first team. The following month, he signed for Conference South side Welling.

In the summer of 2009, Lee signed for AFC Hornchurch but the following month, he was released and joined Ryman Leaguers Aveley. Lee moved to Met Police at the end of October 2009. In May 2010, he signed for Malden and Tiptree United.

In November 2011, he moved to Brentwood