"I am most grateful for the many digital messages of goodwill I have received and would like to thank you all for your kindness," she wrote.
The monarch, whose milestone birthday was marked with numerous events, signed off the rare message "Elizabeth R".
The Queen sent her first ever tweet in 2014 when she opened a new exhibition at the Science Museum in London.
Britain's longest-serving monarch celebrated her 90th birthday on 21 April, and a host of events were held over three months, from April to June.
Her official birthday this year was 11 June and the annual Trooping the Colour was held on Horse Guards Parade, followed by a flypast by the Royal Air Force which the Royal Family watched from the balcony of Buckingham Palace.
The following day the Queen hosted the Patron's Lunch, a street party for some 10,000 people along The Mall which recognised her patronage of more than 600 organisations in the UK and around the Commonwealth.
