She is set to miss the National Service of Thanksgiving, in London.
Buckingham Palace reports Her Majesty has taken the decision ‘with great reluctance’.
The source added that the 96-year-old experienced ‘some discomfort’ during todays Platinum Jubilee celebrations.
She will still attend a beacon lighting event at Windsor Castle this evening, the palace said.
The Queen is believed to have experienced episodic mobility issues during todays events.
It is understood the decision was considered regrettable but sensible due to the length of the journey and time involved and the physical demands the service would require.
The Buckingham Palace statement said: ‘The Queen greatly enjoyed today’s Birthday Parade and flypast but did experience some discomfort.
‘Taking into account the journey and activity required to participate in tomorrow’s National Service of Thanksgiving at St Paul’s Cathedral, Her Majesty with great reluctance has concluded that she will not attend.
‘The Queen is looking forward to participating in tonight’s beacon lighting event at Windsor Castle and would like to thank all those who made today such a memorable occasion.’