Public Health England (PHE) said the woman is being assessed by medical experts while a decision is made about whether to bring her back to the UK.
The MoD said the worker is currently being treated in a specialist treatment centre in Kerry Town.
Up to 700 British military personnel have been working in the west African country to aid the crisis.
Scottish nurse Pauline Cafferkey survived the highly contagious disease after contracting it while treating patients in Sierra Leone last year.
A PHE spokesman said: “We can confirm that a UK military healthcare worker in Sierra Leone has tested positive for Ebola.”
More than 9,960 people have died from the outbreak, according to figures from the World Health Organisation.