Grogan unsuccessfully contested the North Yorkshire seat of Selby at the 1987 general election against the Conservative MP Michael Alison, losing by 13,779 votes. He again contested the seat for the second time at the 1992 General Election but was again defeated by Alison by 9,508 votes.
Between the 1987 and 1992 elections, he also stood unsuccessfully to become a Member of the European Parliament for York in 1989.
Grogan was then elected to the House of Commons at the 1997 general election for Selby. As the incumbent Alison had retired at the election, he defeated the former Conservative MP for West Lancashire, Kenneth Hind, who had lost his seat in 1992, with a majority of 3,836. He made his maiden speech on 7 July 1997.
He led the campaign to save the Selby Coalfield in 2002. In 1999, he called for a memorial to the heroism of women during World War II to be remembered on the empty plinth in Trafalgar Square, with the campaign gaining the backing of the then Speaker of the House of Commons, Betty Boothroyd, and the Princess Royal. Although the campaign was unsuccessful a monument has since been erected in Whitehall.
In the 2005 general election, he retained his seat with a reduced majority of 467 votes, making the seat the 15th most marginal Labour-held seat in the UK. During his time as in parliament, Grogan served as a member of the Northern Ireland Select Committee from 1997 until 2001, and then again from 2005 until 2010.
In 2009, Grogan gained national coverage for his campaign against the proposed options for the privatisation of Royal Mail.
He campaigned against the proposed expansion of Heathrow Airport, the top-up tuition fee reforms in 2004 and voted against the UK's involvement in the Iraq War in 2003. While serving as an MP, he also campaigned for reform of the licensing laws, and public service broadcasting. Grogan also campaigned for the protection of the rights of agency workers, and access for all to sporting listed events on free-to-air TV.
He was also the chairman of the All-Party Parliamentary Groups on the BBC, Beer and Mongolia.
While serving as the MP for Selby, Grogan also supported the building of a new by-pass for Selby, as well as a new hospital and the expansion of its flood defences.
In 2006, Grogan confirmed he would not contest the next general election after boundary changes were made to his Selby Constituency.
In 2013, Grogan was selected as the Labour candidate for Keighley for the 2015 general election. He lost to the Conservative candidate Kris Hopkins by a margin of 3,053 votes. He refought the seat in the 2017 general election, winning with a majority of 249 votes.