Joined by the Duke of Edinburgh she visited the charity's new operating base at the Egerton-Smith Centre at Cambridge Airport.
The royal couple were given a tour by the Duke of Cambridge who has been based in the city for more than a year.
They viewed one of two operational H145 helicopters before unveiling a plaque.
The Queen and the Duke of Edinburgh also met some of the charity's medics, support staff and pilots.
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Launched as a charity in 2000 the organisation's pilots fly an average of five missions per day from bases in Cambridge and Norwich and cover a wider geographical area spanning Norfolk, Suffolk, Cambridgeshire, Essex, Bedfordshire and Hertfordshire.
The monarch was at the base for about 40 minutes before heading to Buckingham Palace, where she is due to meet outgoing Prime Minister David Cameron.
The Queen has opened the new base of the East Anglian Air Ambulance (EAAA) where her grandson works as a helicopter pilot.