Lee joined the team of trainer Howard Johnson permanently in 2002, after leaving the stables of Malcolm Jefferson and was largely responsible for the schooling and on-track development of horses owned by Graham Wylie[1] including Inglis Drever, No Refuge and Arcalis.

[6] Lee missed the 2006 Scottish National due to a virus,[7] which would eventually end his relationship with Howard Johnson for whom he had been the main stable jockey.

Lee rode favourite Joe's Edge in the 2007 National, but pulled up at the 20th fence after failing to trouble the leaders.

[citation needed] Although his profile dipped sharply after joining Murphy, he came back into the sport's consciousness through his involvement with several improving chasers and hurdlers, and moved into second place in the 2007–08 jockeys championship.

Noel Meade – After a successful stint on the Irish pony circuit, Lee left school at the age of 15 to join the stable.

Bill Haigh – Here, recovering from his severe injury problems, Lee rose to the top ten in the jockey championship.

Malcolm Jefferson – A successful stint for Lee which secured him the lucrative position with Howard Johnson, and fifth place in the jockey championship.

J Howard Johnson – With this stable, Lee secured the top jockey award at Cheltenham and a Scottish Grand National win.

Lee suffered a spinal injury on 10 November 2023 when unseated from mount Ben Macdui at Newcastle Racecourse.