The two heads of state spoke via telephone just over a year since their last meeting, when the US President flew to the UK in early June 2019 for a state visit.
Calls of this nature are made at the request of the Government and it is not known for how long the Queen and the president spoke or the topics under discussion.
But a tweet posted on the official royal family account said: “Today, The Queen spoke to President Trump by telephone from Windsor Castle ahead of Independence Day in the United States on the 4th July.”
The Queen has held telephone conversations with a series of world leaders during the coronavirus lockdown.
These phone calls include with France’s President Emmanuel Macron, Australia’s Prime Minister Scott Morrison and Justin Trudeau, Canada’s Prime Minister.
Mr Trump’s conversation with the Queen came ahead of his country’s Independence Day celebrations on July 4.
The US leader’s three-day state visit began on June 3 last year and he was welcomed to the UK by the Queen during a ceremony at Buckingham Palace.
Additional reporting by Press Association.