The young Princess arrived at the service alongside her older brother Prince George, their mother Kate, Princess of Wales, and the Queen Consort Camilla.
King Charles III and Prince William entered the chapel walking behind the Queen’s coffin.
The Duke and Duchess of Sussex were also seated nearby and at one point he caught Charlotte’s eye as she adjusted her hat.
He gave a touching smile to his young niece, who is known in the family for being outgoing and determined.
It was not known if George and Charlotte would walk in the procession in Windsor as their names were not featured in the order of service.
However, the two elder Cambridge children were both present at the chapel after the funeral at Westminster Abbey.
They joined the 2,000 other royals and heads of state who gathered at the Abbey to say goodbye to Britain’s longest-reigning monarch.
The children walked in the procession through the Abbey flanked either side by their parents, in a change to the originally suggested formation.
George naturally did as his sister told him, bowing his head as a mark of respect as the coffin went by.
It was a long day for the royals as there was a private burial service held on Monday evening for the family.
It was one of the only parts of the historic day not to be televised.