The East African nation has among the harshest anti-LGBTQ laws in the world, and anyone convicted of engaging in homosexual acts faces life imprisonment.
The legislation has drawn widespread criticism outside the country and prompted the World Bank to halt loans to Uganda earlier this month.
Several people have been arrested this month for allegedly engaging in same-sex activity.
The man charged with aggravated homosexuality appeared in court on 18 August in the eastern city of Soroti, Jacquelyn Okui, spokesperson for the state prosecutors, told the AFP news agency.
She told Reuters he will remain in custody until his case is heard by the High Court, given it was a capital offence.
His lawyer, Justine Balya, told Reuters she felt Uganda’s anti-gay laws were unconstitutional and were currently being challenged in court.
She gave no further details of the case, except to say it was the first aggravated homosexuality charge before the courts.
Uganda has not carried out an execution since 2005, but capital punishment has not been abolished.