Ms Cafferkey was originally infected while working in Sierra Leone in December 2014 and spent almost a month in an isolation unit at the Royal Free Hospital in London.
She was released after making a recovery but fell ill again in October last year and was again treated at the Royal Free for meningitis caused by Ebola.
Now after contracting the bug again, she has been re-admitted to the specialist unit in the British capital which has the UK”s only high-level isolation unit used for treating infectious diseases.
The move reflects the grave risk to her life the virus is once again posing.
Last time she was ill with the disease the Scottish nurse was described as “critically ill” but was discharged in November and transferred to Glasgow”s Queen Elizabeth University Hospital to continue her recovery.
She was later returned home.
A spokesman for the Royal Free Hospital 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 now 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 general public remains low and the NHS has well-established and practised infection control procedures in place.”
She contracted the deadly virus while working as a nurse at the Save the Children treatment centre in Kerry Town, Sierra Leone.
Ms Cafferkey, from South Lanarkshire, was diagnosed after returning to Glasgow from the west African country via London.
At the time of her re-admission last year, Dr Michael Jacobs, from the Royal Free, described the situation as “unprecedented”.
The World Health Organisation (WHO) said Ms Cafferkey was the only known Ebola survivor to develop meningitis months later.
Dr Jacobs, infectious diseases consultant at the hospital, told a press conference in October: “This is the original Ebola virus she had many months ago which has been inside the brain, replicating at a very low level, and has now re-emerged to cause this clinical illness of meningitis.
“This is an unprecedented situation.”
The WHO declared the Ebola outbreak over last year after the deaths of thousands of people but two new cases emerged in Sierra Leone in January.
The organisation called for a “critical period of heightened vigilance”.
When Ms Cafferkey 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.”