Phil Brown started taking his coaching badges while playing for Bolton, encouraged by Bruce Rioch. His first coaching role was as an assistant to Sam Allardyce at Blackpool. He returned to Bolton after his playing career ended and served as assistant manager to Colin Todd. Following Todd's departure in September1999, he took charge of the team as caretaker manager, winning four games out of five, until the appointment of Sam Allardyce. He then served as Allardyce's assistant for six years, before deciding to forge his own career as a manager.
Brown's first full time senior management position was at Derby, where he succeeded George Burley in June 2005. His time at Derby proved to be unsuccessful and he was sacked just seven months into his tenure in January 2006 and replaced by Terry Westley. Derby was in 19th place when Brown departed and in 33 league and cup matches Derby had won 7 drawn 14 and lost 12.
Brown was appointed as first-team coach at Hull City on 27 October 2006 under Phil Parkinson, and took over as joint caretaker manager alongside Colin Murphy on 4 December 2006 after Parkinson's sacking.
Hull was in 23rd position with 17 points from 21 matches and 5 points of safety. With three wins and a draw in the six matches as caretaker manager took Hull to 21st position with 27 points from 27 matches, he was appointed as the permanent manager of the club on 4 January 2007.
Hull finished the season in 21st position on 49 points and with the ten points deduction for Leeds, Hull were 7pts clear of a relegation place. Brown’s record in League and Cup matches was won 9, drawn 6 and lost 12 in 27 matches.
The following season Hull won promotion to the Premier League for the first time in the club's 104-year history, by beating Bristol City at Wembley in the Championship play-off final on 24 May 2008. His League and Cup record for the 2007/08 season was won 26, drawn 12 and lost 15 in 53 matches.
The first nine games Hull spent as a top division club resulted in six wins as they occupied third place in the Premier League and were only being kept off the top by Liverpool and Arsenal having superior goal difference. Hull finished in 17th position one place and one point above relegation.
On 15 March 2010 Brown was put on gardening leave at Hull after a run of four defeats left the team in the relegation zone. Hull achieved one win in the last fifteen games under Brown, and a total of five in the 2009/10 league season. His contract as manager was confirmed ended on 7 June 2010, by which time the Tigers had been relegated under new manager Iain Dowie.