Pauline Cafferkey was readmitted to an isolation unit at the Royal Free Hospital in London earlier this month after suffering an apparent relapse.
Health officials confirmed she had been diagnosed with meningitis caused by Ebola and had a "long recovery ahead".
The 39-year-old, from South Lanarkshire in Scotland, contracted Ebola in Sierra Leone.
Dr Michael Jacobs, who is treating her at the Royal Free Hospital in London, said: "Pauline has become unwell by meningitis caused by the Ebola virus. But to be very clear about this, she hasn't been re-infected with the Ebola virus.
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"I'm really pleased to tell you that in the last few days she has made a significant improvement. She is much better now. I think she has a long recovery ahead of her and will be with us for quite a while still."
A total of 65 close contacts of the nurse have been identified, with 40 of those offered vaccinations as a precaution.
The Ebola outbreak in west Africa has killed 11,312 of the 28,457 people infected since December 2013, according to the latest WHO figures.