Seen as the final step in the division of the couples’ public duties, Harry and Meghan are breaking away from the Royal Foundation.
It follows reports over the past year of a rift, first between Kate and Meghan, and then between future king William and his younger brother, Harry.
Sources denied there was a feud, saying it was “largely about preparing both couples for their future roles, which are obviously on divergent tracks”.
William and Kate will remain with the original charity, which will be renamed the Royal Foundation of the Duke and Duchess of Cambridge.
The statement on the Royal Foundation said: “Later this year the Royal Foundation will become the principal charitable and philanthropic vehicle for The Duke and Duchess of Cambridge.
“The Duke and Duchess of Sussex will establish their own new charitable foundation with transitional operating support from The Royal Foundation.”
It added: “These changes are designed to best complement the work and responsibilities of Their Royal Highnesses as they prepare for their future roles, and to better align their charitable activity with their new households.”
The Royal Foundation said the decision was made following the conclusion of a review into its structure.
It said both couples will continue to work together in the future, including on the Heads Together mental health campaign.
Harry and Meghan have already split from the Cambridges’ Kensington Palace household, setting up their own at Buckingham Palace in the spring.
Royal aides previously said the foursome were to remain joint patrons of the Royal Foundation.
The Sussexes, who have recently welcomed baby son Archie Mountbatten-Windsor, also moved from London’s Kensington Palace - home to William and Kate and their children - to live at Frogmore Cottage in Windsor.
Thursday’s announcement followed William and Harry’s meeting with trustees of the Royal Foundation at Kensington Palace on Wednesday to finalise the arrangements.
They were not joined by the duchesses, but both dukes spoke, addressing the board.
William, Kate, Harry and Meghan’s joint Royal Foundation venture was intended to harness the star power of the four high-profile royals, but it lasted just 16 months.