The Queen has yet to meet Theresa May in 2017
Her Majesty had called her regular meeting of her privy council at her Norfolk estate last Thursday to discuss a number of issues currently affecting the country and notably Northern Ireland.
Secretary of State for Northern Ireland James Brokenshire MP, Home Office Brandon Lewis MP Minister of State, Secretary of State for Culture, Media and Sport and Karen Bradley MP were called in for the formal discussions with the monarch.
However, University of Edinburgh educated Ms Rudd, 53, was instructed to arrive early for a private audience with the Queen.
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The Queen usually holds weekly meetings with the PM but has not done so this year
This is the third time the Queen has held a meeting Ms Rudd since December
Her Majesty has not yet met with the Prime Minister this year with their last discussion during a meeting held at Buckingham Palace on the evening of December 13.
A source said: "The meeting was entirely private, The Queen asked for an audience with Ms Rudd ahead of her usual privy council.
"A number of issues were raised and this is the first senior level meeting she has had with the Government for more than a month.
Amber Rudd and Theresa May share a joke ahead of an audience with the Queen
"This is the third time the Queen has held a meeting Ms Rudd since December.”
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The Queen has notably changed the time of her usual weekly meetings with the Prime Minister from day to evening now Mrs May has taken over.
The Prime Minister and the Monarch usually meet once a week at Buckingham Palace. However, they have not done so for more than a month or since the Government has returned to work following recess.
The Queen met the Privy Council last Thursday but has still to meet Mrs May
When David Cameron was PM the pair usually met in the morning.
Last week's privy council meeting was not attended by the Foreign Office secretary Boris Johnson despite the US elections taking centre stage.
Mr Johnson has not yet had an official sitting with the Queen since taking over his position as Foreign Secretary.
However, the Queen did instruct her Alistair Harrison, Marshal of the Diplomatic Corps, to bid a formal goodbye to the US Ambassador Matthew Barzun who relinquished his appointment as Ambassador to the Court of St. James's.
Amber Rudd has been invited to meet the Queen three times since December
It has been reported Queen Elizabeth could be set to invite new president Donald Trump for a state visit to the UK.
Mr Trump was said to be hopeful of a meeting with the Queen after she was described as the country's "secret weapon" in attracting him.
Plans were said to have been drawn up in Whitehall.
A formal invitation is reported to be being formulated after he was sworn in as president.
Queen Elizabeth II in pictures
Wed, December 21, 2016
Queen Elizabeth II making her Royal visits in her many colourful and elegant outfits.
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The Queen pictured in December 2016
A source told the Sunday Times: "The government has decided that their secret weapon to get in with Trump is to offer him an early visit to the Queen, him and [his wife] Melania staying at Windsor Castle."
Another cabinet source said: "The Queen is the key here. She's not a secret weapon, she's the biggest public weapon you have. Nigel Farage can't get [Trump] in front of the Queen."
A spokesman for Buckingham Palace confirmed the private audience took place however would not be drawn on the content of the discussions.
The Home Office refused to comment.