According to our reporter in Gulu Steven Okello, Kyagulanyi was taken quietly to court in the presence of only two lawyers.
Among his clients was Kassiano Wadri, Kyagulanyi's favoured candidate in the by-election who went on to win Wednesday's vote despite being in police custody. Wine's driver was later shot dead.
Kyagulanyi was arrested following campaign violence in Arua Municipality in which President Museveni's convoy was attacked by opposition supporters.
He has not been seen in public since he was detained. As rights groups demand his release, his lawyer says his client has been so "brutalized he can not walk, he can not stand".
On Friday, police patrolled Kyagulanyi's Kamwokya constituency in the capital Kampala, breaking up groups of protesters demanding his release.More news: Trump says in 'no rush' to get NAFTA deal
A group of four opposition MPs and 30 others who were arrested at the same time as Kyagulanyi appeared in a civilian court in Gulu to be charged with treason. "It is hard to say whether he understands this and that".
Many Ugandans expressed concern for Kyagulanyi's safety after Uganda's deputy prime minister told legislators he had been admitted to hospital in custody, without giving details.
Ssentamu's driver was shot dead in the clashes.
In a statement Thursday, Museveni said he supported the court action against the politicians. Segona, the lawyer for the defendants, told the magistrate some of the accused had been "badly beaten and tortured during the process and after arresting them" by soldiers.
Once considered a marijuana-loving crooner, the 36-year-old "ghetto child" is a new member of parliament who urges his countrymen to stand up against what he calls a failing government.More news: Chievo v Juventus: What To Expect From Cristiano Ronaldo's Serie A Debut
In hotly contested by-elections this year, he has backed candidates who emerged victorious, signalling his rise in ranks of the political opposition.
Although Museveni has campaigned on his record of establishing peace and stability, some worry that those gains are being eroded the longer he stays in power.
The alleged harassment of Ssentamu, however, has only boosted his popularity and led to calls for a presidential run in 2021.
Museveni, who took power by force in 1986, is now able to rule into the 2030s.
Museveni, who is 73, is now able to seek re-election in 2021 because parliament passed legislation previous year removing a clause in the Constitution that had prevented anyone over 75 from holding the presidency.More news: United Kingdom parliament attack suspect charged with attempted murder