2005 Parliament

Fitzpatrick was re-elected in the 2005 general election, and was then appointed a junior minister in the Office of the Deputy Prime Minister, then John Prescott, with the role of Minister for London, a role he took with him on his subsequent move to the Department of Trade and Industry in May 2006. In 2007, he argued against a CWU strike saying it would harm their cause.

On 29 June 2007, he moved to become the Parliamentary Under-Secretary of State at the Department for Transport, with shipping, aviation and road safety amongst his responsibilities,^[5] and was replaced as Minister for London by Tessa Jowell.

In 2008, during the Christmas period, Fitzpatrick and his wife visited Bangladesh, touring the development projects supported by the Canary Wharf Group. The purpose of the trip was to re-visit the country since 1999, and see the regeneration projects that this group supports. During his visit, he visited the Football Academy in Dhaka, also to Jagannathpur and Sylhet, where many Bangladeshis in the UK originate from including many in his constituency.^[6] Fitzpatrick was promoted to Minister of Department for Environment, Food and Rural Affairs^[1] in the June 2009 reshuffle. He kept this role until Labour's defeat at the 2010 General Election.

In August 2009, Fitzpatrick left a wedding at the London Muslim Centre when he was told it would be segregated by gender. In a local newspaper article, he blamed the Islamic Forum Europe for encouraging segregation, though the couple claimed Fitzpatrick had "hijacked [the wedding] for political gain". Fitzpatrick stated he had left the wedding as discreetly as possible: "it was never my intention to offend Mr Islam and if he thinks that I done so then of course I will apologise to him".^[7]

2010 Parliament

Following boundary changes, Fitzpatrick contested the newly created Poplar and Limehouse constituency in 2010, and was returned with a 4.7% swing to Labour, contrary to the national swing against the party.

He was campaign manager for former Labour MP Oona King (Baroness King of Bow) in her failed attempt to be endorsed as the Labour candidate in the 2012 London Mayoral Election.^[8] From 2010 until his resignation in 2013, he served as Shadow Minister of State for Transport,^[9][10] covering aviation, shipping and road safety, his former ministerial brief. Fitzpatrick was a parliamentary supporter of Labour Friends of Israel.^[11]

In August 2013, he resigned from his front bench role as Shadow Transport Spokesman in order to vote against both Labour and Government motions on the use of chemical weapons in Syria^[12] stating he was "opposed to military intervention in Syria, full stop".^[13]

2015 and 2017 Parliament

In December 2015, Fitzpatrick voted for the use of UK air strikes in Syria against ISIS.^[14]

Fitzpatrick was one of 13 MPs to vote against triggering the 2017 general election.^[15]

Fitzpatrick has spoken of a desire to implement the decision of the 2016 Brexit referendum and was one of five Labour rebels to support Theresa May's Brexit deal in March 2019;^[16] he has voted against proposals for softer forms of Brexit such as EEA membership,^[17] against party colleague Yvette Cooper's amendment to delay Brexit to avoid no deal, and for then chair of the Conservative 1922 Committee Graham Brady's amendment to weaken the Northern Irish backstop.^[18]

In June 2019, he announced that he would not stand for re-election to Parliament, having said that the 2017 general election would be his last election.^[19]