Rosdeep Kular, who was charged under her married name of Adekoya, appeared from custody at Edinburgh Sheriff court accused of murdering her son and attempting to defeat the ends of justice.
His body was discovered in Fife on Friday after he was reported missing from his home in the north of Edinburgh.
The 33-year-old appeared shortly before 4pm in a brief private hearing, before Sheriff Frank Crowe, that lasted a few minutes.
She made no plea or declaration, was remanded in custody and committed for further examination .
Mikaeel was reported missing from his home in the Drylaw area of the Scottish capital on Thursday morning.
Police Scotland issued his picture and appealed to the public for help in finding him.
Hundreds of volunteers from the local community joined police and specialist teams as they searched the surrounding area on Thursday and Friday.
Coastguards also scoured the shoreline a mile from his home.
But in the early hours of Saturday Assistant Chief Constable Malcolm Graham revealed that the body of a young boy had been discovered in Fife, and that a woman had been detained.
Investigations were focused in an area of woodland behind a house in the Fife town of Kirkcaldy.
The boy's mother, who is understood to be estranged from her husband, was formally arrested and charged in connection with her son's death later on Saturday.
More than 500 calls were made to a dedicated phoneline set up in the wake of Mikaeel's disappearance.
Floral tributes, soft toys and candles were placed at a small park near his home.
About 500 people turned out on Saturday night for a memorial service at Muirhouse St Andrew's Church, less than a mile from the home Mikaeel shared with his twin sister and three other siblings.
Kular is expected to make a second appearance at the court on Tuesday January 28.