Mills became Bradford City's first £1 million player when Paul Jewell purchased him in preparation for the 1998–99 season. Mills made a large contribution to Bradford's promotion to the Premier League, becoming the club's top scorer with 24 goals. He also scored on his return to Vale Park, perhaps with a point to prove after a Vale programme article described him as "poor" and his touch as "frequently awful". The 1999–2000 season was a poor one for Mills, scoring just six goals he was troubled with injury and had a falling out with manager Paul Jewell. He spent March 2000 on loan with First Division Manchester City. His poor form left him labelled as a "forgotten man" when he scored twice in the 2000 UEFA Intertoto Cup against Lithuanian side FK Atlantas. New manager Chris Hutchings put Mills on a list of seven "underachievers", with a warning that a continuation of poor form would see those players released. Hutchings' reign would last only a further four months. However, in that time Hutchings had sold Mills to Portsmouth for a club-record £1.25 million, to make way for Ashley Ward. Pompey later struggled to pay the fee and were put on a transfer embargo by the FA.