Breaking the news on social media, the chef said that the Michelin-starred restaurant will close its doors on 31 July.
"Thank you to all our loyal customers, staff, supporters and suppliers," he wrote. "It has been a rollercoaster of a ride and wonder journey but it’s time for us to say goodbye.
"Please come and visits us as we bid farewell to one of the iconic restaurants in London."
The announcement comes amid speculation that Atherton is planning a number of new projects in the capital, including a venture in Mayfair with Spencer Metzger, who stepped away from his role as head chef at The Ritz in August last year.
Pollen Street Social opened in April 2011 and was named the best new UK restaurant by the Good Food Guide 2012, entering its list of the UK’s Top 50 Restaurants at number eight.