The 45-year-old actress was recognised for her services to drama in the New Year's Honours list.
Bonham Carter was accompanied by director partner Tim Burton and stood before Queen Elizabeth II wearing a striking red tartan dress and miniature top hat.
In 2010, the Les Miserables star received an Academy Award nomination for playing Her Majesty's mother in The King's Speech.
Her co-star Colin Firth, who played the Queen's father George VI, collected a CBE from Prince Charles last month.
Bonham Carter declined to speak to reporters after the ceremony.
She said back in January that she would accept her CBE on behalf of her severely disabled father Raymond.
"I always thought my father deserved a medal for facing 25 years of chronic disability with quiet daily heroism so I am delighted to accept such a wonderful honour in his memory," she said.
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