The boys, from Walton, Liverpool, will face a youth court at South Sefton Magistrates' Court in Bootle today. They are thought to be the youngest children in modern times to face accusations of murder.
They are accused of the abduction and murder of James and the attempted abduction of a second two-year-old boy. The attempted abduction accusation is understood to relate to an incident earlier on the day of James's disappearance.
Emotions have been running high in the area since James's body was found on 14 February. The boy from Northwood, Kirkby, had vanished two days earlier after wandering from his mother's side in Bootle.
There were a series of arrests as disturbances erupted after a 12- year-old boy was arrested during the murder hunt last week. He was eliminated from the inquiry, but has had to go into hiding with his family under assumed names.
Since then the situation has been peaceful, after appeals from both the police and James's heartbroken family.
Superintendent Paul Burrell said: 'I would ask the communities, the community leaders and the clergy, with whom we work so closely, to continue to show and encourage the level of compassion and dignity which so typifies them. We ask all of Merseyside to remain calm as by doing so we can greatly assist the legal process.'
Police are planning a low-key policing operation outside the court, but will have reinforcements standing by.
Youths are trying to cash in on the murder with a bogus charity collection. Police said they were knocking on doors in Liverpool asking for money for the James Bulger Appeal for child victims of crime. No house-to-house collections had been authorised.