The group, a mix of students and activists, were arrested while taking part in a protest two weeks ago against a new education bill.
They face possible jail terms on charges including insulting civil servants and refusing to disperse.
Video of the protests showing people being cornered by police and beaten sparked international condemnation.
President Thein Sein of Myanmar (formerly Burma) has defended the action of officers, telling the BBC that in many Western countries a similar situation might have ended in gunfire and death.
In addition to the 65 people in court in the town of Letpadan on Wednesday, another five have been charged in absentia. Eleven people who were released on bail will be charged at a later date.
All could face jail terms of up to six years.
The BBC's Jonah Fisher, at the court, says relatives and supporters gathered outside the building with flowers, water and food for the detainees. Riot police were deployed to keep back the crowds.
Our correspondent says that while there have been reforms in Myanmar since the end of military rule, the case shows that its laws and legal system remain dated and repressive.
The students began a protest march from Mandalay to Yangon (also known as Rangoon) in January, in opposition to a bill which centralises control over higher education.
They were calling for more power to be devolved to universities and higher education institutions, the right to form student unions, and teaching in ethnic minority languages.
The march was technically illegal as it did not have official approval.  The two sides had been in negotiations, and the authorities had agreed to let the students continue to Yangon.
But the students were angered by police opposition when they reached Letpadan, 140km (90 miles) north of Yangon, and clashes broke out as they attempted to break through police lines.
Scores of students and some police officers were injured, while more than 100 people were arrested.
The government has announced an inquiry into the response of the security services, state media report. Young Burmese have been at the forefront of several protests in Myanmar over the years, including a notorious 1988 uprising against the former ruling junta.
Sixty-five people have appeared in court in Myanmar to be charged over a student protest that ended in violence.