The chef joined D&D from the now-closed Manchester House in January to head up the 300-cover dining room.
In an announcement D&D did not give a reason for his departure but said the restaurant was having a “highly successful first year of business”.
“We are really pleased with what we have created at 20 Stories; it got off to the most incredible start and every day goes from strength to strength,” said Des Gunewardena, CEO of D&D London.
“Revenues have been way above our expectations. Aiden has obviously played a significant part in the success of 20 Stories and we would like to thank him very much for his contribution .We offer him our very best wishes for the future.”
A spokesperson for D&D added that the date of Byrne’s departure and details of his replacement were not yet confirmed.
Byrne also runs The Church Green pub in Lymm, Cheshire.
He oversaw Manchester House from 2013-17. The restaurant’s owners Living Ventures closed the restaurant and it entered administration last month after struggling with difficult summer trading.