Fulham took over Murphy's Tottenham contract on 31 August 2007.

Murphy cemented himself as a regular starter, kept his place in the team throughout the season and scored six goals in 43 matches.
One goal, a rare header scored on 11 May 2008, gave Fulham a 1–0 win away at Portsmouth and ensured their Premier League survival at the expense of Birmingham City and Reading; the goal was scored as manager Roy Hodgson prepared to substitute Murphy.
Following the match, Murphy highlighted Hodgson's "key role" in the team's avoiding relegation.
Murphy signed a new one-year contract, with an option for a further year, at the end of the season, and was appointed club captain for 2008–09.

On 9 November 2008, Murphy scored his 100th goal at club level from the penalty spot, as Fulham beat Newcastle United 2–1.
Murphy scored another penalty as, for the first time in 45 years, Fulham beat title-chasing Manchester United at home.

The year's option on Murphy's contract was taken up during the season, but in August 2009, amid reported interest from clubs including Birmingham City and Stoke City, he signed another extension, until June 2011.
Murphy missed two months in the early part of the season with a knee ligament problem, but went on to captain Fulham to their first European final.
They eliminated opponents including Juventus, defending champions Shakhtar Donetsk, Bundesliga champions Wolfsburg, and Hamburg to reach the 2010 UEFA Europa League Final.
Ahead of the semifinal, Murphy said that just reaching the final "would be one of the greatest achievements of our history".
Fulham lost 2–1 to Atlético Madrid to a goal scored just four minutes from the end of extra time.

The 2010–11 season started without Hodgson, who left for Liverpool, and was replaced by Mark Hughes.
In October, Murphy made a controversial comment about managers responsible for dangerous tackles made by players.
His comment was supported by some, but received heavy criticisms from other managers.
In response to these criticisms, Murphy said his comments "were blown out of all proportion".
In late-January 2011, Murphy signed another contract extension that will extend until 2012.
Just one day after signing a new contract, Murphy scored his first goal of the season and then another, as Fulham beat his former club Tottenham 4–0 in the fourth round of the FA Cup.
Murphy was praised by Manager Mark Hughes for helping the club turn things around and avoid relegation.

Ahead of the 2011–12 season, Murphy believed he could play a major role and declared himself "fitter than ever".
After making forty-nine appearance and scoring seven times in all competitions, he was released by Fulham at the end of the 2011–12 season as he and Martin Jol, who had replaced Hodgson's successor, Hughes, could not agree on a contract extension.
In his last season at Craven Cottage, Murphy created more goalscoring chances than any other player in the top-flight.
Fulham took over Murphy's Tottenham contract on 31 August 2007.
Murphy cemented himself as a regular starter, kept his place in the team throughout the season and scored six goals in 43 matches. One goal, a rare header scored on 11 May 2008, gave Fulham a 1–0 win away at Portsmouth and ensured their Premier League survival at the expense of Birmingham City and Reading; the goal was scored as manager Roy Hodgson prepared to substitute Murphy. Following the match, Murphy highlighted Hodgson's "key role" in the team's avoiding relegation. Murphy signed a new one-year contract, with an option for a further year, at the end of the season, and was appointed club captain for 2008–09.
On 9 November 2008, Murphy scored his 100th goal at club level from the penalty spot, as Fulham beat Newcastle United 2–1. Murphy scored another penalty as, for the first time in 45 years, Fulham beat title-chasing Manchester United at home.
The year's option on Murphy's contract was taken up during the season, but in August 2009, amid reported interest from clubs including Birmingham City and Stoke City, he signed another extension, until June 2011. Murphy missed two months in the early part of the season with a knee ligament problem, but went on to captain Fulham to their first European final. They eliminated opponents including Juventus, defending champions Shakhtar Donetsk, Bundesliga champions Wolfsburg, and Hamburg to reach the 2010 UEFA Europa League Final. Ahead of the semifinal, Murphy said that just reaching the final "would be one of the greatest achievements of our history". Fulham lost 2–1 to Atlético Madrid to a goal scored just four minutes from the end of extra time.
The 2010–11 season started without Hodgson, who left for Liverpool, and was replaced by Mark Hughes. In October, Murphy made a controversial comment about managers responsible for dangerous tackles made by players. His comment was supported by some, but received heavy criticisms from other managers. In response to these criticisms, Murphy said his comments "were blown out of all proportion". In late-January 2011, Murphy signed another contract extension that will extend until 2012. Just one day after signing a new contract, Murphy scored his first goal of the season and then another, as Fulham beat his former club Tottenham 4–0 in the fourth round of the FA Cup. Murphy was praised by Manager Mark Hughes for helping the club turn things around and avoid relegation.
Ahead of the 2011–12 season, Murphy believed he could play a major role and declared himself "fitter than ever". After making forty-nine appearance and scoring seven times in all competitions, he was released by Fulham at the end of the 2011–12 season as he and Martin Jol, who had replaced Hodgson's successor, Hughes, could not agree on a contract extension. In his last season at Craven Cottage, Murphy created more goalscoring chances than any other player in the top-flight.
Danny Murphy (footballer, born 1977)