Mullins began his career with Division 1 side Crystal Palace in 1996, and signed his first professional contract with the club in 1998. He quickly established himself in the first team, and made 257 senior appearances for Palace in five seasons. In October 2003, he switched to First Division side West Ham United, initially on a short-term loan, which quickly turned into a permanent transfer. He remained at the club for five-and-a-half years, making 213 appearances, before joining Premier League side Portsmouth in January 2009. He made 129 appearances for Portsmouth, but the club's financial difficulties meant that he joined Championship side Reading on loan in March 2012. At the end of the 2011–12 season, Mullins left Portsmouth, and joined Birmingham City on a free transfer. After two years, during which he also spent time on loan at Notts County, Birmingham confirmed he would be released when his contract expired at the end of the 2013–14 season.
Mullins made three appearances for the England under-21 squad in 1999.
Mullins was born in Reading, Berkshire. He joined Crystal Palace as a trainee in August 1996, and made his first-team debut in July 1998, at the age of 19, in the 1998 Intertoto Cup matches against Turkish club Samsunspor. Head coach Terry Venables gave him his domestic debut in a 3–3 draw against Bolton Wanderers in August 1998, and he scored his first senior goal in a 3–1 away defeat to Birmingham City a week later. He immediately established himself in the first team, made 45 league and cup appearances in the 1998–99 season, was named "Player of The Year", and was capped for the England under-18 team. Mullins later acknowledged his debt to Venables, saying, "I learnt a lot from him. He took a lot of time with us on the training pitch. He taught us a lot about shape and formation, he's very detailed in that respect. He's very good man on man, he made me feel totally comfortable he didn't pressure me into it at all."
Financial difficulties meant that Crystal Palace were unable to make new signings for the 1999–2000 season and relied on youngsters such as Mullins and Clinton Morrison and veterans such as Andy Linighan as they successfully battled against relegation from Division One. Mullins made 49 league and cup appearances in that season and a further 51 appearances in the 2000–01 season as Palace reached the semi-final of the League Cup but narrowly escaped relegation. He was transfer listed in October 2000 due to what manager Alan Smith described as a "bad attitude" but was taken off the list and was offered and signed a new four-year contract two months later as his relationship with Smith improved. Smith said of him in January 2001, "He's a really good footballer which means I can play him in any position. I like my young players to play in different positions. This season he's played full-back, midfield and sweeper. [We've] got to work on his defending, but he's got pace, he has good vision and he wants to play football."
Mullins made a total of 47 appearances in league and cup in the 2001–02 season as Palace made an ultimately unsuccessful push for the Division One play-off places. He was made captain in the 2002–03 season by manager Trevor Francis, who saw him as an integral part of the squad. He made 52 league and cup appearances as Palace reached the quarter-finals of the League Cup and recorded a memorable 2–0 win over Liverpool in an FA Cup fourth round replay at Anfield. He was named "Player of The Year" for a second time in 2003.
An offer of £600,000 from Birmingham City in January 2003 was rejected as "derisory". With one year remaining on his existing contract, Mullins turned down the offer of a new contract in May. His agent said, "It is no secret that Hayden believes he will not be able to fulfil his true potential at Palace. If the club wishes to get some financial reward for their role in his up bringing, then they need to sell him this summer." The following October, he joined West Ham United. Mullins made over 250 league and cup appearances for Palace, scoring 20 goals.
Mullins was the first signing for West Ham's newly appointed manager, Alan Pardew, and initially joined on a short-term loan to enable him to play against Nottingham Forest on the same day. The deal was made permanent a day later for a fee of £600,000, rising to £800,000 should West Ham be promoted. Pardew said of him, "...I have captured a player that I feel is going to add significantly to us. [He] can play in various positions and give us cover in a number of those [...] I think ultimately he is a central midfield player for us and I think his energy will be important; he will have to battle in the midfield. He is someone we are going to look to when we are up against it, to win the battle and give the room to [other players] to play. He is very much a destroyer and I think we are desperate for one of those."
Mullins made 34 league and cup appearances in his first season for West Ham, helping them to the Division One play-off Final in May 2004, where they were beaten by a single goal to nil by Mullins' former club Crystal Palace. The following season, Mullins made 44 league and cup appearances as West Ham again reached the play-off final, this time beating Preston North End 1–0 to win promotion to the Premier League.
West Ham exceeded expectations in the 2005–06 season, finishing in a mid-table position and reaching the FA Cup Final, which was won by Liverpool 3–1 on penalties. Mullins, having made 42 appearances in that season, was suspended for the final along with Liverpool's Luis García, after the pair had been sent off in a league fixture a few weeks earlier and an appeal against his dismissal was rejected by the Football Association. Pardew said, "I feel very aggrieved and very upset because Hayden has had a fantastic season. He has been one of our best players. He was my first signing here, I'm very proud of him, of what he has done and achieved."
At the beginning of the 2006–07 season, West Ham completed the signing of Argentine international Javier Mascherano who, like Mullins, was a defensive midfielder. However, after a brief period on the bench, Mullins re-established himself in the first team and scored the winning goal, in a 2–1 home win over Blackburn Rovers in October 2006, which put an end to the worst run of results for West Ham in 74 years.
Mullins made 32 league and cup appearances in the 2006–07 season as West Ham narrowly escaped relegation. On 1 November 2008, he scored his first league goal of the season in a 1–1 draw against Middlesbrough at the Riverside Stadium. It was his first league goal for two years.
Mullins made a total of 213 appearances for West Ham, scoring 7 goals.
On 25 January 2009, Mullins joined Portsmouth on a three-and-a-half-year contract. He started the 2010 FA Cup Final in an unfamiliar left-back role as Portsmouth were narrowly beaten 1–0 by Chelsea.
Portsmouth were relegated at the end of the season, but Mullins stayed at the Fratton Park side and took number 8 for the 2010–11 season after captain Marc Wilson was given number 6. He scored his first goal for the club in a 3–1 win over Bristol City on 28 September 2010. He was voted Portsmouth Player of the Season for the 2010–11 season.
On 15 March 2012, Mullins signed for Reading on loan until the end of the season. He made seven appearances for Reading as they were promoted to the Premier League. In the same season his parent club, Portsmouth were relegated from the Championship to League One, so Mullins experienced both promotion and relegation in the same season.
On 12 July 2012, Mullins signed for Birmingham City on a two-year contract on a free transfer. He made his debut in the League Cup first round against Barnet, and kept his place for the opening match of the 2012–13 Football League season, a 1–1 draw at home to Charlton Athletic. He scored his first goal for Birmingham in a 2–2 draw with Nottingham Forest on 15 September.
On 31 January 2014, Mullins joined Notts County on loan until the end of the 2013–14 season. He made his debut the next day as a second-half substitute as County lost 2–0 away to Preston North End. With one match of County's season remaining, Mullins was recalled by Birmingham to cover for the injured Tom Thorpe. Playing at centre back, he made a crucial clearance in the final game, away at Bolton Wanderers, that contributed to Birmingham retaining their Championship status via Paul Caddis's stoppage-time equaliser. Birmingham confirmed he would be released when his contract expired at the end of the 2013–14 season. He finished his Birmingham career having scored twice in 39 appearances in all competitions.
On 5 June 2014, Mullins rejoined Notts County on a one-year contract.
Mullins made three appearances for the England under-21 team in 1999, against Poland in March, Hungary in April and Bulgaria in June.
After retiring from football, Mullins joined Reading in a role that sees him oversee the development of the club's players who are out on loan. In July 2016 he joined Watford as assistant to under-21 coach Harry Kewell.As of end of 2014–15 season
PortsmouthFA Cup runner-up: 2010