The Scottish nurse, who has already beaten Ebola twice, nearly died from meningitis the last time she was admitted into hospital.
The reason behind the latest admission remains a mystery but NHS Greater Glasgow & Clyde pointed to “further investigations.”
She has been rushed to a RAF Herucles plan to be moved to London”s Royal Free Hospital.
The unlucky nurse arrived at the airfield inside an incubation unit.
A hospital spokesman said: “Under routine monitoring by the infectious diseases unit, Pauline Cafferkey has been admitted to hospital for further investigations.”
Ms Cafferkey, 39, was infected with the virus while working in Sierra Leone in December 2014.
She had been treating patients in the West African country at the height of the outbreak which killed more than 11,000 people.
The nurse was rushed back to Britain during what was the deadliest occurrence of the disease since its discovery.
Ms Cafferkey spent almost a month in an isolation unit at the Royal Free Hospital in London.
She was released after making a healthy recovery and even returned to work as a public health nurse at Blantyre Health Centre in South Lanarkshire in March.
However, she fell ill again in October last year and was again treated at the Royal Free, this time for meningitis caused by Ebola.
Doctors said Ms Cafferkey had been treated with “a highly experimental” anti-viral drug in the early stages of development but remained uncertain whether it had been helped her.
At the time, Dr Michael Jacobs, from the Royal Free, described the resurgence of the Ebola virus as “unprecedented”.
He said: “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.”
Medics said the heroic nurse was “critically ill” during this episode which took a month to recover from.
She was transferred to Glasgow’s Queen Elizabeth university hospital to continue her recovery and later returned home.
Dr Derek Gatherer, from Lancaster University, explained: “In areas of the body where the immune system is not particularly active, the Ebola virus can survive in very small quantities.”