The service will deliver information on preventative care, health tips and breaking news bulletins specific to the region about the virus in French and English, and often in audio formats.
"We thought how we could use mobile technology to reach as many people across the continent as possible," Trushar Barot, apps editor at BBC World Service and BBC Global News, told Journalism.co.uk.
The BBC has set up a WhatsApp account which users can add to their contacts. A dedicated World Service producer will send three messages a day as push notifications directly to the user's phone, in a similar manner to the service provided during the Indian elections earlier this year.
"One of the things we learned [from the Indian elections project] was that short audio clips worked really effectively," Barot said, "as people can download and play them at their leisure and share them easily."
Adult literacy rates are still relatively low in Guinea (41 per cent), Sierra Leone (43 per cent) and Liberia (60 per cent), where the epidemic is most intense, so Barot said audio clips could be a more effective way of spreading important information quickly.
Audio could also be more effective than video in terms of the type of smartphone or feature phone used by the target audience, the low bandwidth in some areas, and the prevalence of small data packages on mobile services.
Barot said the team will seek to use images whenever possible as well, with ease of distribution and understanding being the main objectives in combating the spread of the deadly Ebola virus and raising public awareness.
Ebola has so far killed more than 4,000 people in West Africa, where mistrust of health workers and governments in the early stages of the outbreak hampered efforts to control it.
Mobile phone use is relatively high in the region though, and media development organisations like Radar have already been using the power of mobile to help people in remote areas.
Barot said this kind of public service work is "an essential part of what the BBC does".
"It's very important to provide answers" in terms of the journalism, he said, but also to use "the power of our distribution channels to do some public good."
The new WhatsApp service is available on +44 7702 348651.
Update: This article has been updated with figures for Ebola-related deaths in West Africa
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