The girls, aged 15, 16 and 17 are currently in prison awaiting trial for scribbling on a picture of President Pierre Nkurunziza in textbooks, activists said Thursday.
Judges said the three girls should be "prosecuted for contempt of the head of state", and ordered them to a juvenile section of a prison in the north of Burundi at Ngozi to await trial, said FENADEB, a civil society umbrella group of 48 organisations.
It was not clear when they might face trial, but the father of one of the girls said they were already "too scared to eat", according to Lewis Mudge, from Human Rights Watch (HRW).
"With so many real crimes being committed in Burundi, it's tragic that children are the ones being prosecuted for harmless scribbles," HRW's Mudge added.
"Authorities should focus on holding perpetrators of serious rights violations to account instead of jailing schoolchildren for doodles."
The trio has been in custody since March 12, when they were arrested with three other schoolgirls and a 13-year old boy.
The boy was released immediately because he was below the age of criminal responsibility, while the three girls were released without charge.
The girls are accused of defacing photographs of Nkurunziza in five textbooks belonging to their school, but teachers pointed out that the books are shared among all the pupils as there are not enough for everyone to have their own.
A judicial source, who called the case "very sensitive" and said it was overseen directly by the Attorney General, reported that the girls arrived at the prison on Wednesday afternoon.
In 2016, several schoolchildren were handed prison sentences for similar scribbles on the president's face, and hundreds of pupils expelled, sparking an international outcry.