Her Majesty was given a tour of the Bond Street station site, accompanied by various politicians and dignitaries and senior project executives.
She was presented with a commemorative Elizabeth roundel and also met a selection of engineers, construction workers, train drivers and apprentices.
Queen Elizabeth II became the first reigning monarch to travel on the London Underground in 1969, when she opened the Victoria line service.
Transport secretary Patrick McLoughlin said: “Given Her Majesty the Queen's long association with UK transport, it is very fitting that this vital link across our capital will be named the Elizabeth Line in her honour.”
Queen Elizabeth II already has a park in east London and a bridge at Dartford named after her.
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