The commemorative doll, which is priced at £94.99 at the retailer, is now being resold on eBay for as much as £1,000.
Barbie unveiled the doll in April to mark the Queen’s 70 years on the throne, which makes Her Majesty the longest-ruling monarch in British history.
It makes up part of the toy brand’s Tributes Collection, which honours famous and historical figures.
Her Majesty, in Barbie form, dons a white gown with a sash bearing pink and blue ribbons with miniature medallions inspired by the Royal Family Orders.
The doll also wears the Queen’s signature coiffed hair, complete with a tiara based on Queen Mary’s Fringe Tiara, which the monarch wore on her wedding to Prince Philip.
She comes in a box inspired by Buckingham Palace, which showcases the throne and red carpet inspired by the palace’s throne room.
According to the Guardian, John Lewis said its stock of the doll sold out in three seconds.
On eBay, dozens of listings of the collectible doll have gone up, with resellers promising that unopened and impeccable packaging.
But even the listings that do admit to damaged packaging are selling for hundreds of pounds, with one such reseller asking for £999 for the doll in a “slightly damaged box”.
Barbie’s tribute to the Queen is just one of hundreds of Platinum Jubilee merchandise and branding that have become available in recent months.
The market for royal memorabilia can be lucrative, with some rare pieces over the years racking up hundreds of pounds in value.
A spokesperson for Barbie said of the commemorative doll: “Since 1959, the Barbie brand’s purpose has been to inspire the limitless potential in every girl and remind them they can be anything.
“That message has never been more relevant than it is today.”
The Queen’s Platinum Jubilee will be marked with a four-day bank holiday weekend that is set to take place in the UK from 2 to 5 June, which will involve nationwide celebrations and initiatives.