As a professional, Brown played at full back for many years with Hartlepool United, followed by a spell at Halifax Town (with fellow north-easterner Billy Ayre at both clubs and under him at the latter),[3] In 1988, he moved to Bolton Wanderers, winning the Associate Members Cup in 1989.

Following Todd's departure in 1999, he took charge of the team as caretaker manager, winning four games out of five, until the appointment of Sam Allardyce.

[8] Brown was rewarded with a new three-year contract, which he signed on the weekend of Hull City's first ever top-flight match, a 2–1 victory over Fulham on 16 August 2008.

The remainder of the season was not so easy for Brown, as the team struggled to pick up the remaining points necessary to avoid relegation, and he was involved in several controversial incidents.

Our 4,000 travelling fans deserved some kind of explanation for the first-half performance and it was difficult for me to do that from the confines of a changing room.

[17] On 17 March 2009, Brown claimed that he saw Arsenal midfielder and captain Cesc Fàbregas spit at the feet of his assistant manager Brian Horton following Hull's 2–1 FA Cup defeat and elimination at the Emirates Stadium.

[18] After the game Brown also falsely claimed that Arsenal manager Arsène Wenger had refused to shake his hand at one of their two previous meetings that season.

[19][20][21] Brown faced his third improper conduct charge of the season in relation to comments he made about referee Mike Riley after the Arsenal match.

At the end of the game, Brown went onto the pitch with a microphone and started singing (a modified version of) "Sloop John B" to the crowd.

Brown did manage to sign Seyi Olofinjana, Jozy Altidore (on loan from Villarreal), Kamel Ghilas, Stephen Hunt, Paul McShane, and he also signed Ibrahima Sonko on transfer deadline day on loan from Stoke City – after the departure of Michael Turner to Sunderland.

Brown's position as Hull manager was thought to be under threat in November 2009 following a poor start to the season, however a run of eight points from four games dampened such speculation.

[25] The team's disciplinary problems also continued, with a £40,000 fine levied following a fracas in a 3–0 defeat at Arsenal and Hull also occupying last place in the Fair Play League.

[26] 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.

[33] Having reached the 2013 Football League Trophy Final under Sturrock, Southend lost 2–0 at Wembley on 7 April under Brown, to Crewe Alexandra.

[39] On 12 March 2018, following his spell at Southend, Brown was appointed the manager of League Two side Swindon Town until the end of the 2017–18 campaign.

Brown warned that the club were "facing oblivion" following poor results and angry confrontations between Southend chairman, Ron Martin and supporters.

[56] On 10 January 2024, Brown was appointed manager of National League bottom club Kidderminster Harriers on a contract until the end of the season.

[57] Despite having overseen an initial upturn in form, winning six of his first eight matches in charge,[58] Brown was unable to prevent the club being relegated.