Rosdeep Kular, 33, appeared in a private hearing at the Edinburgh Sheriff's Court under her married name Rosdeep Adekoya. She is also accused of attempting to defeat the ends of justice.
Kular did not enter a plea and was remanded in custody and committed for further examination at a further hearing on January 28, Scotland's Crown Office and Procurator Fiscal Service said.
She had reported her son Mikaeel Kular missing from their family home in Edinburgh last Thursday morning, triggering a massive search operation.
She was charged after almost 24 hours of questioning.
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Forensic teams have been working throughout the weekend at the back of the bungalow where the body was discovered. It is now the home of Pandeep Kular, Mikaeel's aunt and Rosdeep Kular's sister.
Kular, a beauty therapist and mother of five, told police that she put her son to bed in her flat in Edinburgh at 9pm on Wednesday, but when she went to wake him up at 7:15am the following morning he was missing.
Hundreds of local residents joined in the search operation.
However, mystery surrounds the little boy's final weeks in light of the discovery of his body just yards from the bungalow in Kirkcaldy where Kular used to live earlier.
Mikaeel had not been seen at his nursery school in Edinburgh since it broke up for the Christmas holidays on December 19.
He failed to return when term resumed on January 7, apparently because he was suffering from a chest infection.
Meanwhile, police in Hampshire and Derbyshire arrested two men, aged 19 and 26, yesterday on suspicion of posting racist messages on Twitter relating to Mikaeel's disappearance.
They were both questioned and released on police bail.