[15][16] Following the decision of Ian Blackford to stand down as the SNP Westminster Group Leader, Flynn announced his candidacy for the role, defeating Alison Thewliss 26–17 in a vote of Scottish National Party MPs.

[21] Flynn's leadership came at a time of a cost of living crisis and when the United Kingdom's Supreme Court set out that the Scottish Parliament does not have the devolved competence to hold an independence referendum without the consent of the British Government.

First Minister Nicola Sturgeon had set out plans for the next election to the House of Commons to be a proxy referendum on independence, putting the Frontbench Team at the centre of a constitutional campaign within Scotland.

In February 2024, Flynn was highly critical of the role of the speaker of the House of Commons Lindsay Hoyle during a parliamentary debate on a Gaza ceasefire motion.

[25] As a result, Flynn unveiled a new much slimmed down frontbench including himself, Pete Wishart as his deputy and Kirsty Blackman as chief whip.

The alleged "hit list", which included Collette Stevenson, Jackie Dunbar, Emma Roddick, Evelyn Tweed, and Karen Adam, was reported to have been drawn up at Flynn's direction by Aberdeenshire North and Moray East MP Seamus Logan.

[30][31] Flynn's plan to potentially hold a dual mandate - known as double jobbing in British politics - sparked significant controversy: SNP rules require MPs to resign Westminster seats before seeking Holyrood selection, and the SNP had previously criticised Scottish Conservative Party leader Douglas Ross for double jobbing.

In particular, Joanna Cherry and George Adam criticised the decision, while incumbent MSP Audrey Nicoll reaffirmed her intent to run.