Trudeau expressed his condolences from Vancouver, where he has been at a three-day cabinet retreat. Canada announced a 10-day mourning period and lowered the flag on Canada's parliamentary buildings to half-mast.
"It is with the deepest of sorrow that we learned today of the passing of her majesty Queen Elizabeth II," Trudeau, dressed in a dark suit, said in remarks to reporters on Thursday.
"She was our Queen for almost half of Canada's existence. And she had an obvious deep and abiding love and affection for Canadians."
"She was one of my favourite people in the world and I will miss her so."
The Queen died in Scotland surrounded by some of her family members, Buckingham Palace said on Thursday.
Elizabeth's eldest son Charles, 73, automatically becomes king of the United Kingdom and the head of state of 14 other realms, including Canada.
His wife Camilla becomes Queen consort.
Although Canada ceased being a colony of Britain in 1867, it remained in the British Empire until 1982, and is still a member of the Commonwealth of former empire countries that have the British monarch as head of state. A British-appointed governor-general acts on behalf of the monarch.
The Queen visited Canada more than any other country during her reign - 23 times as part of royal tours over the course of 70 years.
James Smith Cree Nation, which witnessed one of Canada's worst ever incidents of mass violence on Sunday, resulting in the death of 10 people, received this week one of Queen Elizabeth's last letters of condolence, one of the chiefs told reporters on Thursday.
While the Queen remained popular among Canadians, support for the monarchy has dropped in recent years.
An opinion poll from the Angus Reid research group in April showed that 51 per cent of Canadians thought the country's constitutional monarchy should be abolished in coming generations, up from 45 per cent in January 2020.
