Wetherall's start to the 2001–02 season was hampered by a groin injury and his first full game of the campaign came on 14 September 2001 when he scored in a 5–1 Division One victory over Gillingham, which put Bradford second in the table. A groin injury again kept Wetherall out of the side for nearly five months, during which time he was linked with moves back to the Premier League at either Southampton or Manchester City, but he opted to stay at Valley Parade. He returned from injury for a reserve game in March after four months out with just over two months of the season left. He returned to the side against Burnley in a game noted for Paul Gascoigne's debut for Burnley, and scored in his next game as Bradford eased any relegation worries by defeating Crewe Alexandra 2–0. He played in the club's final seven games and was named club captain for the following season after Stuart McCall left the club.