Rosdeep Kular, 33, appeared in a private hearing at the Edinburgh Sheriff's Court. She is also accused of attempting to defeat the ends of justice but made no plea or declaration.
The case was continued for further examination, with another court appearance expected on January 28.
Kular was detained on Friday night and arrested and charged on Saturday after Mikaeel Kular's body was found in a woodland behind her former home in Kirkcaldy, Fife, where she lived before moving to Edinburgh.
Kular reported her son missing from their family home in Edinburgh last Thursday morning, triggering a massive search operation.
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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.