Phil Brown finished his playing career in 1996, having been a full-back for Hartlepool United, Halifax Town, Bolton Wanderers and Blackpool. He became Sam Allardyce's assistant manager at Blackpool, before returning to Bolton where he would coach for Bruce Rioch. In 1999, Brown was appointed as an assistant manager to Colin Todd at Bolton. When Todd resigned seven matches into the 1999/00 season, Brown took charge for five matches, impressively winning four in the process. Brown was reunited with Allardyce when the latter took over in September that season, and reverted to his role as caretaker manager.

He helped the club to promotion to the top flight in the 2000/01 season via the play-offs. Allardyce and Brown ensured the club avoided relegation in the following two seasons, before Bolton started to become a force. They finished eighth in the 2003/04 campaign and also reached the final of the League Cup, losing 2-1 to Steve McClaren's Middlesbrough. It is unsurprising that Brown names Allardyce as one of the major influences on his managerial career after six years of success.

Brown's good work earned him the chance to take over from George Burley as Derby County manager in June 2005. However, he was sacked just seven months into his tenure after winning only seven of 33 matches. He left with Derby lying 19th in the Championship, although they did go on to avoid relegation. A 3-1 defeat by their FA Cup fourth-round opponents Colchester United spelt the end for Brown.

He was appointed as first-team coach at Hull in October 2006, working under Phil Parkinson. He became joint caretaker alongside Colin Murphy in December of that year after Parkinson was fired by the Tigers. Three wins and a draw in his six matches prompted the club to appoint Brown on a permanent basis at the beginning of 2007. The 49-year-old ensured Hull narrowly avoided relegation in the 2006/07 season as the club finished 19th in the Championship.

Brown led the Tigers to a historic promotion through the play-offs last season, taking several clubs by surprise along the way. He ensured a 3rd place finish, ending the season just four points behind Stoke City who were promoted automatically. The Tigers saw off Watford 6-2 on aggregate in the play-off semi-finals, setting up a meeting with Bristol City in the final. Dean Windass scored the only goal of the match, a magnificent volley, in front of 86703 fans to ensure promotion to the top flight for the first time in the club's history. Brown described this as "the best day of my life."