However a spokesman said she expects to continue light duties at Windsor this week.
A palace source said a number of cases have been diagnosed in the Windsor Castle team.
Her Majesty was being closely monitored after Charles’ caught the virus just days after pair had been in close contact earlier this month.
As the time, Buckingham Palace refused to confirm whether the 95-year-old monarch had tested positive or negative, fuelling fears for her health, but palace sources insisted she was not displaying symptoms of the virus.
However, it has now been confirmed that she too has tested positive for Covid.
The Queen has been triple-vaccinated. She received her first jab in January 2021 and her second jab in March while sources say it is believed she got her booster jab in October.
The Prince of Wales, 73, has finished his period of self isolation after testing positive last Thursday, forcing him to pull out of a joint engagement in Winchester with wife Camilla.