Wetherall kept off his injury problems and played in the first 15 games of the 2003–04 season, but was ruled out for two months after suffering medial ligament damage, following a knee injury sustained during the club's 1–0 defeat to Watford. He returned on 28 December 2003 in a 1–0 victory which gave Bradford their first win in six games. His return to the defence added a second successive clean sheet. The revival in form was short-lived and despite Wetherall missing just one more game, when he sustained a calf injury, Bradford were threatened with another relegation. Wetherall scored a header against Reading in a 2–1 win and gave Bradford a "slim chance" of avoiding relegation, only for that to be confirmed two weeks later after a 3–2 defeat to Wimbledon.