Often referred to by his nickname of "Mad Dog", Allen began his career with Queens Park Rangers, signing professional in 1983 and spending six years at Loftus Road playing in the 1986 League Cup Final defeat against Oxford United, before a £670,000 move to West Ham United. Signed by manager Lou Macari, Allen made his debut on 26 August 1989 in a 3–2 home win against Plymouth Argyle. He scored the second goal, the other West Ham goals coming from David Kelly and Kevin Keen. Under manager Billy Bonds Allen was part of the team which won promotion to the First Division in 1991 and to the Premier League in 1993. Allen was frequently booked during his West Ham career and had a reputation for poor discipline. He was sent off in a match on 17 January 1990 for a two-footed lunge on Derby County's Mark Patterson. During a game on 30 November 1991 against Sheffield Wednesday, managed by Allen's manager at Queens Park Rangers, Trevor Francis, Allen was booked after only 20 seconds of being on the pitch for a jump tackle on Carlton Palmer which saw Palmer carried off with a suspected broken leg. Although not sent-off, West Ham manager Bonds fined Allen a week's wages. During his time at Queens Park Rangers Allen had been refused permission, by manager Francis, to attend the birth of his first child as Allen would miss an important match. Allen attended the birth and was disciplined by the club. Under Bonds and Harry Redknapp Allen formed a successful partnership with Peter Butler with Allen contributing 34 goals from midfield in 234 appearances. However by 1995 team discipline was poor at West Ham and with Allen playing alongside Julian Dicks, John Moncur and Don Hutchison bookings were commonplace. Allen was again dismissed in a match against Queens Park Rangers on 3 May 1995 after fouling Rufus Brevett. He would play only five more games before being allowed to leave.
Allen stayed with the Hammers until September 1995 when he made a £500,000 switch to Portsmouth after a successful loan spell at Fratton Park. After three frustrating years with Pompey, which took in a brief loan stint at Southend United, he hung up his boots and began a coaching career.
Allen began his management career as an assistant manager at hometown club Reading, where he joined Alan Pardew when the Royals were in the relegation zone. The team produced championship form in their closing 20 fixtures, winning 12 and drawing 4 to secure a top 10 finish. Two years later they won promotion to Division One.
Allen's first full manager role was at Conference side Barnet, from March 2003 to March 2004. He succeeded from Peter Shreeves, to whom he was assistant manager from March 2002. Allen built a team from scratch in pre-season of the 2003–04 campaign. The team shot straight to the top end of the table, however Allen left for Brentford with a few weeks of the season remaining in a move that disappointed many Barnet fans. Under the guidance of new manager Paul Fairclough, the Bees made the play-offs but were beaten in the semi-finals by Shrewsbury Town.
Allen had a good run at Brentford, saving the club from relegation from League One in his first season. In the 2004–05 and 2005–06 seasons he took Brentford to the play-offs, but they were eliminated by Sheffield Wednesday and Swansea City respectively. He also took Brentford to the fifth round of the FA Cup in two consecutive years, going out to Southampton in the 2004–05 season, losing 3–1 after a 2–2 draw at St Mary's, and to Charlton Athletic 3–1 in the 2005–06 season. He also was in charge of one of the major giant killings in the fourth round in the 2005–06 season, beating Sunderland 2–1.
At Brentford, he proved to be a very popular manager with the fans and an object of curiosity to opponents and media alike due to his unconventional managerial methods, which seem to have paid off due to the relative success Brentford had under him on a limited budget. For example, he participated in a 25 mile sponsored bike ride on November 2005 to raise funds for Brentford. In May 2006, Allen announced his resignation as manager of Brentford, citing lack of Board commitment to investing in the team to take it to the next level. In July 2006 he completed his UEFA Pro Licence in coaching.
Allen then dropped down a level to manage League Two team Milton Keynes Dons for the 2006–07 season, a club with heavy financial backing and ambitions from owner Pete Winkelman, albeit one that had been in severe decline for the past few years and had dropped from the Championship to League Two in three seasons. Allen managed to arrest the club's decline and took his team to the play-offs, but lost in the semi-finals to Shrewsbury Town.
In May 2007, Allen became the new manager at Championship side Leicester City, after Leicester and Milton Keynes Dons had negotiated a compensation package.
In August 2007, striker Jimmy Floyd Hasselbaink agreed contract terms with Leicester and chairman Milan Mandarić invited him to undergo a medical at Leicester. But when Hasselbaink arrived in Leicester on 13 August, Allen told him that the medical was no longer going take place. Six days later, Mandarić confirmed an interest in striker Derek Riordan, who was lacking first team football at Celtic. However, Allen refused to make an offer for Riordan, which further aggravated Mandarić. Relations with chairman Milan Mandarić quickly deteriorated and his contract was terminated by mutual consent on 29 August 2007 after just four games in charge.
Allen was appointed as manager of Cheltenham Town on 15 September 2008, on a three year contract. His father, Dennis, had been manager at Whaddon Road between 1974 and 1979. With financial difficulties hitting the club and an increasingly troubled dressing room atmosphere, the entire Cheltenham squad were put up for sale. Allen allowed key players to leave mid-season either on loan or for reduced prices, contributing to a run of results which left Cheltenham near the foot of the League Two table. On 20 October 2009 and amidst poor results on the pitch, Allen was suspended by Cheltenham Town and placed on gardening leave pending an internal investigation into allegations that he racially abused a nightclub bouncer. In November Gloucestershire police announced that no action would be taken against Allen concerning the alleged nightclub incident. He remained on leave whilst Cheltenham Town considered his future at the club. On 11 December it was announced he had left the club. In January 2010 he was appointed part-time scout for Queens Park Rangers.
On 23 March 2011, Allen returned to his first managerial club, Barnet, until the end of the 2010–11 season. He was working on an eight game contract but left after only three games, in which Barnet were unbeaten, to take charge of Notts County.
Allen took charge of Notts County on 11 April 2011 signing a one-year rolling contract. Notts County won eight points out of the seven games Allen was in charge of at the end of the 2010–11 season, enough for them to avoid relegation. Allen was named League One Manager of the Month in September 2011 after leading the team to four wins and a draw in the league.
Allen was sacked by Notts County on 18 February 2012.
Allen was appointed caretaker manager of Barnet on 16 April 2012 for the last three games of the 2011–12 season, replacing Lawrie Sanchez. Barnet managed two wins under Allen's managership, finished 22nd and avoided relegation from League Two with a 2–1 win on 5 May 2012 on the last day of the season, against Burton Albion. Following the end of the season, Allen's contract ended.
On 5 July 2012, Allen was appointed manager of Gillingham signing a two-year contract. His first match as Gillingham manager came on 14 August 2012, a 2-1 away win against Bristol City in the League Cup. While at Gillingham, Allen oversaw the Kent side's best ever start to a league season. He also broke the club record for most away wins in a football league season with a 1-0 win over Chesterfield, the eleventh of the season on 23 February 2013. On 6 April 2013 Gillingham secured promotion to League One, Allen's first ever promotion in his career as a manager. They secured the League Two title with a 2-2 draw against AFC Wimbledon at Priestfield on 20 April. On 20 May 2013, Allen was crowned League 2 Manager of the Year by the LMA for his achievements with the club. Allen was sacked by Gillingham in October 2013 after sixteen months in charge. Gillingham had won just two games from eleven played on their return to League One.
Having run his own soccer schools programme across 13 towns while still playing professionally. Allen, a UEFA Pro Licence holder and a graduate of the LMA's Certificate in Applied Management at Warwick University, created the company Pro FC which finds young people with the potential to become footballers. He is also non-exec director of the football charity, Coaching for Hope.