The aide reportedly fell ill and tested positive last week, and Royal Household staff who had contact with the person have been ordered to self-isolate.
It is said the worker was diagnosed with potentially deadly Covid-19 before the 93-year-old monarch moved to Windsor Castle.
The Queen, who has avoided shaking hands during audiences and a recent investiture, has since moved to Windsor Castle earlier than usual for Easter.
She is expected to stay there for the foreseeable future with husband Prince Philip, 98.
It was not known if the Queen had any contact with the employee, who is said to be recovering.
Royal sources said she is in good health as she and the Duke of Edinburgh avoid contact with others.
A source told the Sun on Sunday: “The worker tested positive before the Queen left for Windsor. But the Palace has 500 members of staff so, like any workplace, it’s not inconceivable it would be affected in some stage.”
A spokesman for Buckingham Palace said: “We wouldn’t comment on individual members of staff.
“In line with the appropriate guidance and our own processes, we have taken the necessary actions to protect all employees and people involved.”
After leaving Buckingham Palace on Thursday with her two dorgis in tow, the Queen is now at Windsor Castle with the Duke of Edinburgh.
They are socially distancing with a reduced household for their safety at Windsor Castle in Berkshire.
The advanced age of both the Queen and Philip mean they are more at risk of complications if they catch the Covid-19 illness.
Philip was flown by helicopter from the Sandringham estate where he has been staying in his secluded Wood Farm cottage.(Standard Media)