The East African country announced its latest outbreak on January 30 after the death of a male nurse who tested positive for the virus.
"Good news! The current Ebola Sudan virus disease outbreak has officially come to an end," the health ministry said in a post on the X platform on Saturday.
It added the declaration of the end of the outbreak followed 42 days "without a new case since the last confirmed patient was discharged".
In the post, the ministry did not give the latest total caseload recorded during the outbreak.
In early March when the ministry last reported on the caseload, it said at least ten cases had been recorded with two deaths.
Ebola infections are frequent in Uganda which has many tropical forests that are natural reservoirs for the virus.
The latest outbreak, caused by the Sudan strain of the virus, was Uganda's ninth since the country recorded its first infection in 2000.
Uganda also neighbours the Democratic Republic of Congo which has recorded over a dozen outbreaks, including one in 2018-2020 that killed nearly 2300 people.
The outbreak started in Kampala, a crowded city of about four million that is also a crossroads for routes branching out to eastern Congo, Kenya, Rwanda and South Sudan.
Although outbreaks have been common, health experts say the country has been able to leverage on its experience battling the disease over the years to bring them under control relatively quickly.
Ebola is transmitted through contact with infected bodily fluids and tissue.
Symptoms include headache, vomiting of blood, muscle pains and bleeding.
