Mr Besigye was the main challenger to President Yoweri Museveni in the country's recent general election, which Mr Museveni won by a landslide.
He insists he was the rightful winner of the polls, but Uganda's top court upheld the official result.
"We have been informed by police today that Besigye appeared in court in Moroto and was charged with treason," said his lawyer Erias Lukwago.
Mr Besigye was arrested on Wednesday in downtown Kampala and flown to Moroto, where he has been in custody ever since.
It follows a series of arrests of the opposition leader during the election campaign.
Meanwhile, Mr Museveni was sworn in on Thursday for his fifth elective term, extending his 30-year rule of Uganda.
Foreign observers said the poll had been marred by fear and intimidation.
In a BBC interview, Mr Museveni rejected allegations of vote rigging, and accused Mr Besigye of planning to incite violence.
Responding to criticism from European Union observers that the electoral commission "lacked independence and transparency", Mr Museveni told the BBC's Zuhura Yunus that "those Europeans are not serious".
"Transparency is what we've been voting for," he added.
Mr Museveni, a key ally of the West in the campaign against militant Islamists in the region, seized power in 1986 and is credited with restoring stability to Uganda.
However, critics say he has become increasingly authoritarian.
On Friday, the US said Mr Museveni should "rein in" his security forces after they briefly arrested Mr Besigye, and fired tear gas to disperse his supporters in Kampala.