The directive to close schools two weeks before the end of term has come after the death of eight children from the contagious disease earlier this month.
Uganda has closed schools nationwide to curb the spread of Ebola, despite the health minister insisting that new cases had declined.
The directive to close schools from Friday, two weeks before the end of term, was announced earlier this month following the death of eight children from the highly contagious disease.
But in recent weeks, the number of new infections registered in the capital Kampala and the epicentres of Mubende and Kassanda has declined, said Health Minister Jane Ruth Aceng.
"The major breakthrough in this fight against Ebola for Uganda is that the communities have realised that Ebola is deadly and it kills," she said.
"We encourage the population to remain alert and cooperate with the health teams if we are to win this battle and there are signs Uganda is winning," she added.
Uganda's WHO office said on Thursday that as of November 22, no case had been declared for nine days in Kamapala, 10 days in Mubende and 12 days in Kassanda.
The outbreak has claimed 55 lives out of 141 cases, according to Ugandan authorities, who have imposed lockdowns in Mubende and Kassanda.
The measures include a dusk-to-dawn curfew, a ban on personal travel and the closure of markets, bars and churches.
At a school in Kampala, one parent said he was relieved to take his child home.
"I think this early closure was really necessary, because of the situation, the Ebola situation in the country," said banker Joab Baryayaka.
"We trust they are safer with us than staying at school, where we cannot guarantee the situation."
Since the outbreak was declared in Mubende on September 20, the disease has spread across the East African nation.
President Yoweri Museveni has repeatedly ruled out imposing nationwide Covid-like restrictions.
According to WHO criteria, an outbreak of the disease ends when there are no new cases for 42 consecutive days - twice the incubation period of the disease.
The strain now circulating is known as the Sudan Ebola virus, for which there is no vaccine, although several would-be jabs are heading towards clinical trials.
Ebola is spread through bodily fluids. Common symptoms are fever, vomiting, bleeding and diarrhoea.
Outbreaks are difficult to contain, especially in urban environments.