At Southwark Crown Court, Judge George Bathurst-Norman said he was not attempting to set a precedent of banning children from being tried in crown courts.
However, he said, the facts of the case demanded that the European Court of Human Rights' finding in the case of Jon Venables and Robert Thompson, be taken on board.
He ordered that the two boys, accused of indecently assaulting a 13-year-old girl in July last year, should be tried before a youth court where the power of punishment is less severe.
A clinical psychologist told the court that one of the boys had learning difficulties and that his low IQ meant that he could be "intimidated" by appearing before a jury in an adult court.
The ECHR held last year that intellectual capacity was one factor that should be considered when deciding how children are dealt with by the courts.
Judge Bathurst-Norman said the psychologist's evidence left him no choice but to order that the boy be tried before a youth court. He said that the "interests of justice" demanded that both boys should be tried together