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.

In August 2009, Fitzpatrick left a wedding at the London Muslim Centre when he was told it would be segregated by sex (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".

[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.

[21][22] Admitted as a Freeman of the City of London in 2011, Fitzpatrick was elected to the Court of Assistants of the Worshipful Company of Shipwrights in 2017.

[23] A Younger Brother of Trinity House,[24] Fitzpatrick is an Honorary Associate of the National Secular Society,[25] and in October 2021 was awarded the Freedom of the Borough of Tower Hamlets.