The 95-year-old monarch is said to be in good spirits but disappointed not to be able to carry out the two-day trip, which was due to begin on Wednesday.
The Queen has had a busy programme and hosted a major Global Investment summit at Windsor Castle on Tuesday evening, where she looked cheerful as she carried out her royal duties.
A Buckingham Palace spokesman said: “The Queen has reluctantly accepted medical advice to rest for the next few days.
“Her Majesty is in good spirits and is disappointed that she will no longer be able to visit Northern Ireland, where she had been due to undertake a series of engagements today and tomorrow.
“The Queen sends her warmest good wishes to the people of Northern Ireland and looks forward to visiting in the future.”
The Queen’s decision is understood not to be related to coronavirus.
The nation’s longest reigning monarch is resting at Windsor Castle.
She is still expected at this stage to attend events linked to the Cop26 climate change conference in Glasgow at the end of the month.
On Tuesday, it was revealed the Queen had turned down the Oldie of the Year trophy because she feels she does not meet the criteria, believing “you are only as old as you feel”.
The Queen, who is just five years away from her 100th birthday, is due to celebrate her Platinum Jubilee – 70 years on the throne – next year.
She still keeps a busy diary of events and audiences and deals with her daily red boxes of official papers.
She held two audiences on Tuesday via video link from Windsor Castle, greeting the Japanese ambassador Hajime Hayashi and the EU ambassador Joao de Almeida, followed by the investment summit in the evening.
At the weekend, she enjoyed a day at the races at Ascot, and on Monday held a virtual audience with the new Governor-General of New Zealand.
The Queen’s husband of 73 years the Duke of Edinburgh died in April at the age of 99.
The monarch has been pictured out and about at the Royal Windsor Horse Show and Ascot in the months since, and still enjoys riding her own ponies.
Last week, she used a walking stick for what is believed to be the first time at a major public event when she attended a service marking the centenary of the Royal British Legion.