Winston caused mass devastation across the islands of Fiji and is the worst natural disaster ever to hit the country.
The cyclone which is the strongest ever recorded in the area has left at least 43 people dead and destroyed thousands of homes leaving 62,000 people homeless.
The Royal Commonwealth Society said it welcomed the generous private donation from the Queen.
RCS Director Michael Lake, says it is important in times of natural disasters such as Cyclone Winston that the Commonwealth comes together to offer support.
He added that as Head of the Commonwealth, Her Majesty's best wishes and donation would be most gratefully received.
The Queen sent the following message to the people of Fiji: "As the people of Fiji recover from the devastating impact of Tropical Cyclone Winston, I send my sincere condolences to those who have lost loved ones."
"My thoughts are also with those who have seen their homes and property ruined and are starting the hard work of rebuilding. I know how resilient and resourceful the people of Fiji are" she said