Harris, 84, was jailed last year over 12 counts of indecent assault against four girls in Britain, including the childhood best friend of his daughter Bindi, between 1969 and 1986.
Now the queen has ordered the removal of his CBE, which stands for Commander of the British Empire and is one step below a knighthood.
The news was confirmed by an announcement in the London Gazette, an official British government journal.
"The Queen has directed that the appointment of Rolf Harris to be a Commander of the Civil Division of the Most Excellent Order of the British Empire, dated 17 June 2006, shall be cancelled and annulled and that his name shall be erased from the Register of the said Order," it said.
He is currently serving a jail sentence of five years and nine months.