Army chiefs have also promised British troops in Afghanistan some festive cheer with the promise of a Christmas meal, phone calls home and a possible football match against American allies.
The Queen passed on her best wishes via defence chiefs.
And Prime Minister Tony Blair stressed British troops should be "really proud of themselves" for their achievements in conflicts worldwide.
Warmest wishes
In her message, the Queen said: "The further deployment of British forces to Afghanistan now taking place has reminded us all of the debt we owe to servicemen and women stationed throughout the world, who will be spending this Christmas away from their families.
"I should be grateful if you would pass on my warmest good wishes to them and their families and assure them that they are much in our thoughts and prayers, particularly over this Christmas period."
Meanwhile Mr Blair spoke on British Forces Broadcasting Service (BFBS).
He said: "My message to our armed forces is that Britain is incredibly proud of what you have been doing, what you are going to do".
He focused on those who were on active service and separated from their families at Christmas.
"I would like them to know that people back in Britain appreciate really deeply the things that they do," he said.
Hampers
Major Guy Richardson, British Armed Forces spokesman in Kabul, said there was a job to be done.
But he said: "We shall ensure everyone will have the opportunity to phone family on Christmas Day," he said.
Mr Richardson, who will be away from his young family, said a friendly football match might take place after Christmas Day.
He said mail was also getting through, if a little delayed.
Supermarket giant Tesco has also pledged a food hamper for 14,000 service men and women on operations around the world.
The hampers were delivered to RAF Brize Norton and Portsmouth Naval base last week.
Around 40 Royal Marines are part of the peace keeping force in the Afghan capital but Britain is expected to contribute up to 1,500 troops in the next few weeks.
Afghan leaders are divided over how long the British-led multinational security force should remain in the war-ravaged nation.
Short stay
The country's new premier, Hamid Karzai, said the force was welcome to stay for as long as it takes to restore order.
Defence minister Mohammed Fahim had indicated international peacekeepers were welcome in Afghanistan for no longer than six months.
In his radio message, Mr Blair said he foresaw troops remaining in the region for no longer than a matter of months.
He said British troops were best placed to get the mission started.
"Then after a few months, obviously someone else will take it on," he said.
He anticipated the bulk of British troops in Afghanistan being withdrawn after the "initial phase."
On Osama Bin Laden, the prime minister said it was unlikely the fugitive was "going to do anything other than fight in this situation".