Home Secretary (2024–2025)
Due to the 2023 review of Westminster constituencies, Cooper's constituency of Normanton, Pontefract and Castleford was abolished, and replaced with Pontefract, Castleford and Knottingley. At the 2024 general election, Cooper was elected to Parliament as MP for Pontefract, Castleford and Knottingley with 47.5% of the vote and a majority of 6,630.
Following Labour's victory in the general election, Cooper was appointed home secretary by Starmer in his government on 5 July. On 7 July, after Starmer confirmed that the Rwanda asylum plan had been scrapped, Cooper announced that the Border Security Command would be established in order to help reduce small boat crossings across the English channel.
Following the 2024 Southport stabbings, in which three young girls were killed, Cooper stated that she was concerned by the incident and described the emergency services' response as courageous. Cooper additionally visited Southport the following morning to lay flowers and meet officials and community leaders. Starmer also visited the same day and laid flowers at the scene, and was heckled by some members of the public. Cooper later condemned the riots across England and Northern Ireland following the stabbing. After Axel Rudakubana's guilty plea on 20 January 2025, Cooper announced a public inquiry, stating that the victims' families "needed answers about what had happened leading up to the attack". This was followed by Starmer's promise to overhaul terrorism laws to reflect the type of non-ideological killings characterised by individuals like Rudakubana, stressing the threat from "acts of extreme violence perpetrated by loners, misfits, young men in their bedroom, accessing all manner of material online, desperate for notoriety, sometimes inspired by traditional terrorist groups, but fixated on that extreme violence, seemingly for its own sake". Significant attention was drawn to the anti-radicalisation Prevent programme for failing to accept referrals of Rudakubana on the basis of him lacking a terrorist ideology. Although an emergency review found that Prevent had followed correct procedures on each referral, Cooper concluded "that too much weight was placed on the absence of ideology" in the programme. Cooper announced that there would be a review on the threshold at which Prevent intervenes, with senior lawyer David Anderson being assigned by Starmer as the Independent Prevent Commissioner to perform the review.
The new office of Border Security Commander was established, whose remit would be to lead the new command and its members. The command was launched by Cooper on 7 July 2024. The command would be funded by money previously earmarked for the Rwanda plan and would be responsible for coordinating the activities of Immigration Enforcement, MI5, the Border Force and the National Crime Agency in tackling smuggling gangs which facilitate illegal migrant crossings over the English Channel. A team in the Home Office was tasked with setting out the remit of the command, as well as its governance structure and its strategic direction. Martin Hewitt was appointed to the role of Border Security Commander in September 2024, by the Home Secretary.
Cooper faced a significant backlash over her "immigration crackdown", with critics saying that her plans were "a waste of taxpayer money, lack detail and fail to recognise 'the dignity and humanity of migrants', especially in the wake of recent racist riots that targeted hotels housing asylum seekers across the country", with Amnesty International accusing Cooper of "reheating the Conservative government's rhetoric around border security", and Enver Solomon of the Refugee Council stating that she was "wasting taxpayers' money on expanding detention places." Cooper's Border Security, Asylum and Immigration Bill was criticised by fellow Labour MPs for retaining Conservative era anti-migrant legislation, with Sarah Champion criticising the bill for disqualifying asylum seekers who cross the Channel in small boats from claiming protection from modern slavery, and Nadia Whittome stating the legislation must reverse "powers to detain child refugees for up to 28 days." Later in September 2024 she was likewise also accused of "playing catch-up to Reform".
After a trans rights protest in London she branded messages of trans solidarity on the statues of several influential figures, including South African prime minister Jan Smuts, "disgraceful".
In November 2024, Cooper voted in favour of the Terminally Ill Adults (End of Life) Bill, which proposes to legalise assisted suicide.
In May 2025, Starmer launched a white paper on the topic of immigration with a speech including that the UK risked becoming an "island of strangers", and that high immigration had done "incalculable damage" to society. His language was criticised for its perceived echoes of Enoch Powell's Rivers of Blood speech, and in June, Starmer apologised for his "island of strangers" comment, saying that the phrase "wasn't right" and "I deeply regret using it". Later, Cooper said she had been effectively excluded from launching the immigration white paper, which was a home office policy, by the Prime Minister's Office who wanted it fronted by Starmer, saying "I didn't see what was going to be said or what the announcement was … that was the way that No 10 operated."
On 23 June 2025, after a small group of Palestine Action people broke into RAF Brize Norton and caused criminal damage to military planes, Cooper reported to Parliament that the group was to be designated as a proscribed terrorist organisation.