Born in Billericay, Essex, Harrison, a goalkeeper, started his career at Charlton Athletic without making any first team appearances.

After a £10,000 transfer to Leyton Orient where he played 65 League and Cup games – he moved to Peterborough United for the 2005–06 season, but in July 2006 returned to Barnet as player-coach.

Harrison was released at the end of the 2009–10 season and briefly joined Dagenham & Redbridge as a coach for their successful play-off campaign.

On 2 August 2012, it was announced that Harrison had been appointed permanent goalkeeping coach at Wycombe Wanderers, after a period working at the club on a temporary basis.

On 22 February 2023 Lee Harrison returned to Wycombe Wanderers for the third time as goalkeeping coach following Matt Bloomfield from Colchester United.