Johnson's first goal for Middlesbrough came in a midweek Premier League match away to Bolton Wanderers on 3 May 2006, opening the scoring in a 1–1 draw with "a mazy run from the left flank before curling in a deflected shot". He was playing due to Middlesbrough's involvement in the 2006 UEFA Cup Final, which was to be played a week later as Steve McClaren rested most of the first team squad. On 30 June 2006, he signed a new four-year contract extension.