She was originally infected while working in Sierra Leone in December 2014 and spent almost a month in an isolation unit at the London hospital.
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.
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Pauline Cafferkey has been admitted to hospital for the third time since contracting Ebola
At one point, 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 and later returned home.
However, NHS Greater Glasgow and Clyde said on Tuesday Ms Cafferkey was in a stable condition at the hospital after "routine monitoring" identified a problem.
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.
GLASGOW, SCOTLAND - FEBRUARY 23: Pauline Cafferkey enters an isolation tent before boarding a RAF Hercules at Glasgow Airport on February 23,2016 in Glasgow,Scotland. The RAFHercules aircraft is transporting her to London where she will be treated at the Royal Free Hospital.. (Photo by Jeff J Mitchell/Getty Images) (credit:Jeff J Mitchell via Getty Images)
(02 of13)
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GLASGOW, SCOTLAND - FEBRUARY 23: Pauline Cafferkey enters an isolation tent before boarding a RAF Hercules at Glasgow Airport on February 23,2016 in Glasgow,Scotland. The RAFHercules aircraft is transporting her to London where she will be treated at the Royal Free Hospital.. (Photo by Jeff J Mitchell/Getty Images) (credit:Jeff J Mitchell via Getty Images)
(03 of13)
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GLASGOW, SCOTLAND - FEBRUARY 23: Pauline Cafferkey enters an isolation tent before boarding a RAF Hercules at Glasgow Airport on February 23,2016 in Glasgow,Scotland. The RAFHercules aircraft is transporting her to London where she will be treated at the Royal Free Hospital.. (Photo by Jeff J Mitchell/Getty Images) (credit:Jeff J Mitchell via Getty Images)
(04 of13)
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GLASGOW, SCOTLAND - FEBRUARY 23: Pauline Cafferkey enters an isolation tent before boarding a RAF Hercules at Glasgow Airport on February 23,2016 in Glasgow,Scotland. The RAFHercules aircraft is transporting her to London where she will be treated at the Royal Free Hospital.. (Photo by Jeff J Mitchell/Getty Images) (credit:Jeff J Mitchell via Getty Images)
(05 of13)
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GLASGOW, SCOTLAND - FEBRUARY 23: Medical staff wearing protective clothing prepare to board nurse Pauline Cafferkey onto a RAF Hercules at Glasgow Airport on February 23,2016 in Glasgow,Scotland. The RAFHercules aircraft is transporting her to London where she will be treated at the Royal Free Hospital. (Photo by Jeff J Mitchell/Getty Images) (credit:Jeff J Mitchell via Getty Images)
(06 of13)
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GLASGOW, SCOTLAND - FEBRUARY 23: Medical staff wearing protective clothing prepare to board nurse Pauline Cafferkey onto a RAF Hercules at Glasgow Airport on February 23,2016 in Glasgow,Scotland. The RAFHercules aircraft is transporting her to London where she will be treated at the Royal Free Hospital. (Photo by Jeff J Mitchell/Getty Images) (credit:Jeff J Mitchell via Getty Images)
(07 of13)
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GLASGOW, SCOTLAND - FEBRUARY 23: Medical staff wearing protective clothing prepare to board nurse Pauline Cafferkey onto a RAF Hercules at Glasgow Airport on February 23,2016 in Glasgow,Scotland. The RAFHercules aircraft is transporting her to London where she will be treated at the Royal Free Hospital. (Photo by Jeff J Mitchell/Getty Images) (credit:Jeff J Mitchell via Getty Images)
(08 of13)
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Medics after transfering nurse Pauline Cafferkey onto an RAF Hercules aircraft at Glasgow Airport before she is flown to London for treatment at the Royal Free Hospital after contracting Ebola. (credit:Andrew Milligan/PA Wire)
(09 of13)
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Medics take their protection suits off after transfering nurse Pauline Cafferkey onto an RAF Hercules aircraft at Glasgow Airport before she is flown to London for treatment at the Royal Free Hospital after contracting Ebola. (credit:Andrew Milligan/PA Wire)
(10 of13)
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The RAF Hercules aircraft carrying Nurse Pauline Cafferkey taxis at Glasgow Airport en route to London for treatment at the Royal Free Hospital after contracting Ebola. (credit:Andrew Milligan/PA Wire)
(11 of13)
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The RAF Hercules aircraft carrying Nurse Pauline Cafferkey taxis at Glasgow Airport en route to London for treatment at the Royal Free Hospital after contracting Ebola. (credit:Andrew Milligan/PA Wire)
(12 of13)
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Medics after transfering nurse Pauline Cafferkey onto an RAF Hercules aircraft at Glasgow Airport before she is flown to London for treatment at the Royal Free Hospital after contracting Ebola. (credit:Andrew Milligan/PA Wire)
(13 of13)
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File photo dated 24/1/2015 of nurse Pauline Cafferkey, who has been admitted to hospital for the third time since contracting the disease, NHS officials have said. (credit:Lisa Ferguson/Scotland on Sunday/PA Wire)