Rosdeep, 33, was detained yesterday after Mikaeel Kular's body was found by officers in woodland behind her former home in Kirkcaldy, Fife, where she lived before moving to Edinburgh.
She was charged after almost 24 hours of questioning, as police confirmed the body was that of her missing son, Mikaeel. The body was removed by officers for a post mortem examination.
Assistant Chief Constable Malcolm Graham, of Police Scotland, said: "Following formal identification, I can now confirm that a 33-year-old woman has been arrested and charged in connection with Mikaeel's death. The woman is expected to appear at Edinburgh Sheriff Court on Monday."
Rosdeep, a mother of five, told police that she put her son to bed at her Edinburgh home at 9pm on Wednesday, but when she went to wake him at 7:15am the following morning he was missing.
She also said that on the night he allegedly disappeared he was sleeping alone in the bedroom he normally shared with his twin sister Ashika.
Officers initially suggested that the little boy may have got up in the middle of the night, put on his clothes, and left the building "for a wander".
For two days, Police Scotland insisted there was no evidence of criminality, and expressed sympathy for Mikaeel's "very distraught" mother.
But the tone of the inquiry changed early on Friday evening when officers admitted for the first time that the child could be the victim of a crime. Hours later, a body was found behind Dunvegan Avenue, Kirkcaldy, in a suburb of the Fife town.
ACC Graham also thanked rescue teams and the public for their help in searching for Mikaeel, BBC reported.
"I would like to again recognise the overwhelming public assistance that Police Scotland have received during the course of this very complex investigation. This includes his family and friends, with whom our thoughts remain," Graham said.
The officer said inquiries were continuing, led by the force's major investigation team.
"I ask that anybody who has any information that they feel would assist the investigation contacts the police," he added.
