Standing 70 meters tall and 15 meters wide, the roughly 400 year-old tree has been Sierra Leone's national symbol for decades.
President Julius Maada Bio called the toppling of the famed tree "a great loss to the nation" as crowds gathered to look at the wrecked trunk.
The "Cotton Tree" was the most important landmark in the West African country which was founded by freed Americans who were enslaved.
It is believed that when those enslaved arrived by boat in the late 1700s, they gathered under its branches to offer prayers before moving into their new home.
"It was regarded as a symbol of liberty and freedom by early settlers," the president wrote on Twitter.
"We will have something at the same spot that bears testament to the great Cotton Tree's place in our history. All voices will be brought together for this."
The "Cotton Tree" has appeared on bank notes, woven into lullabies and visited by royalty, such as Britain's late monarch Queen Elizabeth the II, to mark the country's independence in 1961, according to a statement by Zebek International, a press agency working with Sierra Leone's government.
While the tree had withstood damage throughout the years, including a lightning strike that has left it partially scorched, Wednesday's storm left nothing of the tree but a stump.
FILE - A man walks past the fallen iconic Cotton Tree in Freetown on May 25, 2023.
The kapok tree stood in the middle of a roundabout in central Freetown near the national museum and the president's office.
Passerby Victor Tutu Rogers told Reuters he saw the tree fall around 9:40 p.m. (2140 GMT) on Wednesday, May 24.
"I'm shocked and heartbroken to see our beloved Freetown Cotton Tree destroyed this morning on my way to work," Gibrilla Sesay, a 34-year-old finance worker, told AFP.
In a statement, the Ministry of Tourism and Cultural Affairs appealed to the public not to cut off wood from the debris, which it said would be taken to the national museum.
"In order to preserve the remains of the rich cultural heritage of our beloved city, relics of the fallen tree will be secured and preserved," it said. There were no reports of injuries, the government said.
By Thursday, the branches and debris had been cleared away, leaving only a stump.
"As a municipality it was very much symbolic, the place where we hold our annual thanksgiving every November to offer prayers and for many other events," the city's Chief Administrator, Festus Kallay, said.
"The Freetown skyline will hardly be the same again."
For Sierra Leone, the loss is comparable to the fire that destroyed Paris' Notre Dame cathedral in 2019, said Zebek International, the government's press agency.
Some information in this article was sourced from the Reuters, Associated Press and Agence France-Presse.