She was honouring the 73rd anniversary of its national day which is celebrated on September 9, according to officials from Buckingham Palace.
The spokesperson said the message was sent on the monarch’s behalf by the UK’s Commonwealth and Development Office “as had been done before”.
The Palace explained this was standard practice for independent countries around the world.
They explained: “Her Majesty in all dealings with other Heads of State acts on the advice of the FCDO.”
They added: “As in previous years, HM The Queen has sent a message to the people of the DPRK [Democratic People’s Republic of Korea] on occasion of their National Day.”
The surprising news broke on Monday when North Korea’s state media KCNA released a message which announced the country’s leader had “received a message of greeting from Elizabeth II” on September 7.
KCNA claimed the message read: “As the people of the Democratic People’s Republic of Korea celebrate their National Day, I send my good wishes for the future.”
Kim Jong Un also marked the occasion with a military parade through Pyongyang, where soldiers were seen wearing bizarre Hazmat suits.