Thoronka, who lost most of his family to the virus, applied to stay in Britain and had been offered a sports scholarship by the University of East London (UEL).
But his application “did not meet the required thresholds within the immigration rules,” Britain’s interior ministry said.
“All applications for a visa or leave to remain are considered on their individual merits and in line with the immigration rules,” a Home Office spokesperson said.
The athlete now has until Monday to leave Britain and risks being detained and deported if he fails to do so, according to a report in the Guardian newspaper.
Thoronka was Sierra Leone’s top 100-metre sprinter and was given the Best Male Athlete award by the Sportswriters Association of Sierra Leone.
The Guardian reported he could run 100 metres in 10.5 seconds.
‘One of an elite’
Dusty Amroliwala, UEL’s deputy vice-chancellor and chief operating officer, said the university was “disappointed” by the decision, adding that it would be a “severe test” for the athlete.
“Jimmy’s story – his struggle against huge adversity, his determination to succeed, his fortitude, all in the face of losing his family… these things all marked him out as being a very special young man,” he said.
“He was exactly the kind of individual to whom UEL would wish to extend the hand of support and we are deeply saddened that we are no longer allowed to do so.”
Mike Bense, a coach at the Heathside running club in north London, where Thoronka had been training, said the athlete was “potentially one of an elite”.
“This is a very critical time in his life and he can’t afford to waste any time at this point,” he told the Guardian, adding: “Jimmy has a good support network here and we are part of it.”
Thoronka’s lawyers had submitted a medical report stating that the sprinter was in “a chronic traumatised state” following the death of eight members of his family from Ebola, the Guardian reported.
“What is going to happen to me if I am forced to return to Sierra Leone? There is no one to look after me and support me there and the training facilities are very bad… I don’t think I will make it if I have to go back,” Thoronka told the newspaper.
Sierra Leone is one of the world’s poorest countries and numerous athletes from the West African nation have absconded from the Commonwealth Games in previous years.
The Ebola outbreak, which began in December 2013, infected 28 000 people and killed around 11 300, with Sierra Leone, Liberia and Guinea the hardest hit.