Two workers who have been in close contact with the unnamed woman are also being evacuated, while another two are being tested for the virus in Sierra Leone.
None of the four others have been diagnosed with Ebola but the two returning on Thursday (March 12) will be assessed and monitored for any symptoms during an incubation period.
A specially-equipped RAF C-17 was scheduled to land at the Ruislip base on Thursday afternoon.
The infected female soldier and her two colleagues will then be transferred to London's Royal Free Hospital, in Hampstead, where previous Ebola patients have been treated in isolation.
Dr Jenny Harries, Ebola incident lead at Public Health England, said: “We can confirm that all the appropriate support is being offered to these individuals.
“We would like to emphasise that there is no risk to the general public’s health and the overall risk to the UK continues to be very low.
“Our thoughts are with all the health care workers, and their families, affected at this time.”
Mark Francois, minister for the armed forces, added: “The wellbeing of our service personnel remains our overriding priority. This includes the individual directly affected and their four colleagues, for whom precautionary measures are now being taken.
“I have seen for myself the courage and dedication of our personnel, who are doing such a vital job in Sierra Leone.
“They are helping to protect not only those in west Africa from this unprecedented outbreak, but also us at home by working to combat the spread of the virus.
“We are very proud of what our servicemen and women are doing and our thoughts are with their five colleagues and their families at this time.”
The infected medic is the third British health care worker confirmed to have caught the deadly virus during the recent outbreak in west Africa, which has killed more than 9,800 people in the past year.
The other two, Pauline Cafferkey and Will Pooley, made full recoveries after being evacuated back to Britain.