Atherton, who also worked in Australia for Frank as regional MD, has 15 years' experience in agency PR and has advised clients including Activision, Deliveroo, 20th Century Fox Home Entertainment and Hotels.com.
She replaces former MD Jo Vyvyan-Robinson, who returned to Freuds earlier this year after a short spell at Stir.
London-based Stir currently employs 17 people, and is placed 131st in the 2017 PRWeek UK Top 150 Agencies. It specialises in food and drink, with clients including Nestlé, Heineken and Brown Forman. Stir is part of Captivate, a seven-strong group of creative agencies.
Atherton said: "I am excited to be leading the next chapter of Stir’s story as a leading consumer lifestyle agency and to be doing so with its talented and passionate team, who have already impressed me with their individual capabilities.
"Watch this space for the next steps of the journey, which will harness the potential for truly integrated communications, thanks to working within Captivate Group, and push the boundaries within the consumer, experiential and digital space."
Captivate CEO Chloe Ellis said: "We’re confident Polly will continue to drive Stir’s upwards trajectory in what is set to be a bright and exciting future for the agency."
Stir was founded in 2011 by Alicia Mellish, who departed last year with the appointment of Vyvan-Robinson as MD. Mellish also sold her stake in the business to Captivate in 2017.