"There is a suspected case, samples have been taken from the suspect and we are analysing them," said Ugandan health ministry spokesman Rukia Nakamatte.
The passenger is the first to be tested in east Africa in the current outbreak sweeping west Africa, although Uganda has suffered Ebola outbreaks in the past, most recently in 2012.
The patient was stopped as he arrived in Uganda's main Entebbe airport showing signs of fever, Uganda's Daily Monitor newspaper said, quoting airport officials.
Reports of a case in late July in northern Uganda proved to be a false alarm.
Ebola has claimed at least 932 lives and infected more than 1,700 people since breaking out in west Africa earlier this year, according to the World Health Organisation.
Uganda, with its past experience of Ebola, has sent a medical team to west Africa to help.
Nations across east Africa have said they have boosted measures to combat possible Ebola cases arriving in their countries.
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