Following Hill's retirement from playing the game, he joined former club Rochdale's coaching staff, where he held the position of Director of Youth. On 17 December 2006, Hill was appointed as caretaker manager, following the sacking of Steve Parkin. His first game in charge against Milton Keynes Dons ended a 2–1 loss and they were left in the League Two relegation zone. His first win came 2 games into his reign, a 4–0 win over Boston United, which lifted them out of the relegation zone. After his second 4–0 win, Rochdale appointed Hill as permanent manager on 3 January 2007. Rochdale ended the season in ninth, despite being in the bottom three for the majority of the first half of the season.
In his first full season as Dale boss, he took Rochdale to League Two play-off final, where they lost 3–2 against Stockport County, having defeated Darlington 5–4 on penalties in the semi-final. The 2008–09 season saw Hill take Rochdale to the play-offs for the second year in a row, but they were beaten 2–1 by Gillingham, the eventual winners. The next season saw improvement again, gaining automatic promotion, after a 1–0 win against Northampton Town on 17 April 2010. However, a dip in form near the end of the season saw Rochdale miss out on the League Two title, finishing third behind Notts County and Bournemouth. Rochdale finished ninth in League One the following season. The 68 points gained meant the club had achieved their highest league finish since the 1969–70 season.
Hill was given permission to talk to Championship side Barnsley about their vacant manager's job on 20 May 2011. Four days later, he chose to remain with Rochdale because "we are ambitious but we're also happy in our work here." Hill changed his mind at the start of June and was appointed manager of Barnsley, with assistant David Flitcroft joining him. With a relatively small budget at his disposal, Hill mainly signed players from lower divisions. Rochdale players Matt Done and Scott Wiseman were among his first signings for Barnsley. Barnsley avoided relegation by one place in his first season in charge, with results having deteriorated following the sale of striker Ricardo Vaz Te and long term injuries to influential midfielders Jacob Butterfield, Jim O'Brien and David Perkins in January. Hill was sacked by Barnsley on 29 December 2012, following a defeat by Blackburn.