The queen and her husband Prince Philip greeted the president and US first lady Michelle Obama as their helicopter touched down on the manicured lawns of Windsor Castle, the oldest and largest inhabited castle in the world located about 32 km to the west of the British capital.
After chatting briefly, they climbed into the queen's Range Rover and the 94-year-old Philip drove them to the royal residence, which has been a family home for British monarchs for nearly 1,000 years, as trumpets sounded in the distance.
"I realise there's been considerable speculation - and some controversy - about the timing of my visit," Obama wrote in the Daily Telegraph newspaper. "And I confess: I do want to wish Her Majesty a happy birthday in person."
The main purpose of Obama's visit is to lend his support for Britain remaining in the European Union ahead of a referendum on membership in June.
However, it also gives Obama his third opportunity to meet the queen after a state visit with his wife in 2011, when they stayed at Buckingham Palace, and a private audience in 2009.
Elizabeth, by far the oldest monarch in British history, marked the milestone of reaching 90 with a walkabout on Thursday in Windsor, meeting thousands of well-wishers. Obama himself has previously spoken warmly about the queen, who has met 11 US presidents since acceding to the throne in 1952.
"For nine decades, Her Majesty has been a source of strength and inspiration not only for the people of Britain but for millions of people around the world," Obama said in a documentary for British TV aired last month.
"We often speak of the deep and enduring partnership between our two countries - it is indeed a special relationship - and her majesty has been a vital part of what keeps our relationship so special."
Later on Friday, the president will meet the younger generation of royals when he has dinner with the queen's grandson Prince William and his wife Kate, and William's younger brother Harry at Kensington Palace in central London.