Kizza Besigye, a fierce critic of Ugandan President Yoweri Museveni and once his personal doctor, has faced arrest and assault on previous occasions.
He has contested and lost four presidential elections.
Besigye, who at first appeared in court without lawyers and in a cage, rejected government legal representation and said he should be tried in a civilian court because he is not a member of the armed forces.
The former president of the opposition Forum for Democratic Change (FDC) party also was charged with possessing an illegal firearm, which he denied.
He will stay in custody until December 2 with FDC member Hajj Lutale Kamulegeya, who was also charged and denied wrongdoing.
Besigye's reappearance came four days after he went missing in Nairobi.
On Saturday his wife, UNAIDS executive director Winnie Byanyima, claimed he had been kidnapped and put in a Ugandan military jail.
The Ugandan government has not commented.
Kenyan foreign affairs permanent secretary Korir Singoei told local media that Kenya was not involved in the alleged incident.
Besigye's lawyer, the Kampala mayor and FDC member Erias Lukwago, expressed concern that his client was arrested abroad.
"For his liberty to be curtailed in a sovereign state like Kenya, and no actions being taken by the Kenyan government against the sister country violating the territorial integrity of Kenya, that is a very serious matter and we are not going to let it lie down," he said.
Museveni, who has ruled the east African country since 1986, has long been criticised by human rights groups over alleged violations against opposition figures.
