"Rarely has one person so epitomized the very best of humanity and leadership through selfless public service," Kenya's President, Uhuru Kenyatta, said in a statement noting the former British colony's close ties with the queen.
"The People of Kenya have always had a fondness for the magnificent and graceful twenty-five-year-old royal who visited our country as a Princess and left it as Queen," he said.
Kenya will observe a period of national mourning until sunset on Monday, with the flags at government buildings, military bases, naval vessels and overseas missions to be flown at half-mast for the same duration, Kenyatta announced.
The Kenyan leader, whose father Jomo Kenyatta was the country's first president following independence from Britain in 1963, earlier said he had "received the sad news... with great sorrow and a deep sense of loss."
Kenya "will forever hold Queen Elizabeth II in a special place in our individual and collective hearts", he said.
Kenya's president-elect William Ruto also paid tribute to the queen late Thursday, hailing her "admirable" leadership of the Commonwealth.
"May her memories continue to inspire us. We join the Commonwealth in mourning and offer our condolences to the Royal Family and the United Kingdom," said Ruto.
"She steered the institution's evolution into a forum for effective multilateral engagement," Ruto said on Twitter, describing the bloc as a testament to the queen's "historic legacy".
On the streets of the capital Nairobi, several Kenyans said they were saddened by the news of her death.
"It's a sad day because Kenya was colonized by the British, so Kenyans are part and parcel of the British system," said Vincent Kamondi, a 51-year-old taxi driver.
Although Kenya's Mau Mau freedom fighters suffered horrific abuses under the colonial regime for taking part in one of the British Empire's bloodiest insurgencies, independent Kenya has maintained strong ties with its former rulers.
"The education we have, the religion we have, it came from the British, so it gave us a path of where we are heading to," said businessman Jacob Midam, 38.
Elizabeth was on a visit to the former colony in February 1952 when she received news of her father's death while staying at the Treetops hotel, a remote game-watching lodge in the Aberdare forest.
Kenya was the first stop on the tour of the Commonwealth she had embarked on with her husband, Prince Philip, in place of her ill father.
It was during their night at the Treetops hotel that Elizabeth would become queen, an episode immortalized in the popular TV series "The Crown".
The royal visit -- and the legend to go with it -- made Treetops among the most famous hotels in the world.