The 89-year-old queen was accompanied by her husband Prince Philip, 94, as she visited the site where at least 52,000 people from across Europe died during World War II, including teenage Jewish diarist Anne Frank.
She was due to see a memorial stone to the young girl, whose journal of her family's time hidden from the Nazis during the German occupation of The Netherlands has been read by millions around the world.
The queen is also due to lay a wreath and meet camp survivors and liberators.
At a banquet at Berlin's presidential palace earlier in the week, the queen warned against "division" in Europe, in a speech focused on historical references to the lessons of World War II, the fall of the Berlin Wall and German reunification.
In April, on the 70th anniversary of the camp's liberation, German President Joachim Gauck paid tribute to Britain for restoring "humanity" to the country, saying its forces led by example during the subsequent Allied occupation.
