The 40-year-old was initially admitted to Glasgow’s Queen Elizabeth University Hospital after a routine test by staff at the infectious diseases unit.
As a result of those findings, a specially converted RAF Hercules aircraft later arrived at Glasgow Airport to take her to the Royal Free Hospital.
Ms Cafferkey, a nurse at a clinic in Blantyre, Lanarkshire, was treated in London twice in 2015 after contracting ebola in Africa the previous year.
A spokesman for the Royal Free said: “We can confirm that Pauline Cafferkey is being transferred to the Royal Free Hospital due to a late complication from her previous infection by the ebola virus.
“She will be treated by the hospital’s infectious diseases team under nationally agreed guidelines. The ebola virus can only be transmitted by direct contact with the blood or bodily fluids of an infected person while they are symptomatic, so the risk to the public remains low.”
Ms Cafferkey contracted ebola in Sierra Leone in 2014 after volunteering to join a British medical team in Kerry Town. It is believed a wrongly fitted protective mask allowed her to be in contact with infected body fluids.
She spent almost a month in isolation at the Royal Free at the beginning of 2015 after the virus was detected when she arrived back in the UK. The nurse was later discharged after apparently making a full recovery and in March 2015 returned to work at Blantyre Health Centre.
In October last year, it was discovered that ebola was still present in her body. Health officials later confirmed she had been diagnosed with meningitis caused by the virus. At the time of her re-admission last year, Dr Michael Jacobs, of the Royal Free, described the situation as “unprecedented” while the World Health Organisation said Ms Cafferkey was the only known ebola survivor to develop meningitis months later.
When she was released from hospital for the second time, she said: “I am forever thankful for the amazing care I have received at the Royal Free Hospital. For a second time, staff across many departments of the hospital have worked incredibly hard to help me recover and I will always be grateful to them and the NHS.”
In November, the Royal Free said Ms Cafferkey had made a full recovery from ebola and was no longer infectious. Dr Derek Gatherer, lecturer in biomedical and life sciences at Lancaster University, said: “It is very sad to hear that Ms Cafferkey has once again been admitted to hospital.
“It is now becoming clear that ebola is a far more complex disease than we previously imagined.
“The meningitis that Ms Cafferkey suffered from at the end of last year is one of the most serious complications of all, as it can be life-threatening.
“She was unlucky enough to be one of only a handful of patients in whom it has been seen.”