The agency said no new cases of Marburg, caused by a deadly virus from the same family as Ebola, were reported over the past 42 days after the last patient was discharged following treatment.
The outbreak was declared on 13 February and was the first of its kind in Equatorial Guinea.
A total of 17 laboratory-confirmed cases and 12 deaths were recorded. Another 23 were reported to have died from probable Marburg infection, the WHO said.
The announcement of the end of the outbreak in Equatorial Guinea follows a similar move by Tanzania last week.
Marburg virus is transmitted to people from fruit bats and spreads among humans through direct contact with the bodily fluids of infected people, surfaces and materials.
WHO said it is continuing to work with Equatorial Guinea to maintain measures such as surveillance and testing to enable prompt action should flare-ups of the virus occur.
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