It will be the royal couple's fifth state visit to the country of her ancestors, and comes exactly 50 years after her first.
The state visit will take place over three days, from June 24-26th, although no further information was available from Buckingham Palace or the British Embassy in Berlin on the exact itinerary or venues for the trip.
There has been speculation in the British media that state visits were being scaled back in the wake of the 93-year old Duke of Edinburgh's health, but a Buckinhgam Palace spokesman told the Local that was "categorically untrue."
Previous state visits took place in 1965, 1978, 1992 and 2004. The 88-year old Queen Elizabeth will come this year at the invitation of the German President Joachim Gauck, whose political role is largely ceremonial.
The Queen has made previous, non-state, visits before, visiting Berlin in 1987 and 2000.
The UK press had also speculated that news of the trip was published to distract attention from allegations in the US about Prince Andrew's alleged involvement with an under-age girl, also denied by Buckingham Palace.
News of the royal visit comes just two days ahead of a visit to London by Chancellor Angela Merkel for talks with Prime Minister David Cameron on EU relations, the Ukraine and the situation in Greece.
Gauck and his partner, Daniela Schadt, were guests of the royal family at Buckingham Palace in November 2012.
British Ambassador to Germany, Sir Simon McDonald, said; "It is an honour for me that Her Majesty and His Royal Highness The Duke of Edinburgh will this year come on a state visit to Germany. It will take place exactly 50 years after their first.
"The visit will be an unforgettable event that encapsulates both the width and depth of relations between Germany and the UK."
The Queen has reigned since June 1953, making her the second-longest reigning British monarch after Queen Victoria.
She is descended, on her father's side, from Prince Albert, the consort of Queen Victoria, who was German and known as Prince Albert of Saxe-Coburg and Gotha.
During her 2004 state visit, the Queen attended the reopening of Dresden's historic Frauenkirche, bombed by the Allies during World War Two, and spoke of the "appalling suffering of war on both sides", but stopped short of any apology for the Dresden bombings - one of the most controversial Allied attacks of the war.